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-rw-r--r--gnu/packages/bioconductor.scm7568
1 files changed, 3616 insertions, 3952 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 44bf5c7d24..17d15c06c5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -73,7 +73,7 @@
`((upstream-name . "org.EcK12.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
(synopsis "Genome wide annotation for E coli strain K12")
(description
@@ -103,7 +103,7 @@ analysis.")
(properties `((upstream-name . "org.Bt.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://bioconductor.org/packages/org.Bt.eg.db")
(synopsis "Genome wide annotation for Bovine")
(description
@@ -125,7 +125,7 @@ based on mapping using Entrez Gene identifiers.")
(properties `((upstream-name . "reactome.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://bioconductor.org/packages/reactome.db/")
(synopsis "Annotation maps for reactome")
(description
@@ -148,7 +148,7 @@ database, assembled using data from REACTOME.")
`((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
(synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
@@ -171,7 +171,7 @@ taurus (UCSC version bosTau8).")
`((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
(synopsis "Full genome sequences for Worm")
@@ -196,7 +196,7 @@ objects.")
`((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
(synopsis "Full genome sequences for Worm")
@@ -221,7 +221,7 @@ objects.")
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
(synopsis "Full genome sequences for Fly")
@@ -246,7 +246,7 @@ objects.")
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
(synopsis "Full genome sequences for Fly")
@@ -271,9 +271,7 @@ Biostrings objects.")
`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-dmelanogaster-ucsc-dm3"
- ,r-bsgenome-dmelanogaster-ucsc-dm3)))
+ (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
(home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
(synopsis "Full masked genome sequences for Fly")
(description
@@ -301,7 +299,7 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
(properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
(synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
(description
@@ -324,7 +322,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
`((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
(synopsis "Full genome sequences for Homo sapiens")
@@ -347,7 +345,7 @@ as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
"0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
(properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
(build-system r-build-system)
- (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
+ (propagated-inputs (list r-bsgenome))
(home-page
"https://bioconductor.org/packages/release/data/annotation/html/\
BSgenome.Hsapiens.NCBI.GRCh38.html")
@@ -372,9 +370,7 @@ provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19"
- ,r-bsgenome-hsapiens-ucsc-hg19)))
+ (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
(home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
(synopsis "Full masked genome sequences for Homo sapiens")
(description
@@ -403,7 +399,7 @@ default.")
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
(synopsis "Full genome sequences for Mouse")
@@ -427,9 +423,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-mmusculus-ucsc-mm9"
- ,r-bsgenome-mmusculus-ucsc-mm9)))
+ (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
(home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
(synopsis "Full masked genome sequences for Mouse")
(description
@@ -458,7 +452,7 @@ default." )
`((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
(synopsis "Full genome sequences for Mouse")
@@ -501,7 +495,7 @@ ID and species. It is used by functions in the GenomeInfoDb package.")
`((upstream-name . "GO.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://bioconductor.org/packages/GO.db")
(synopsis "Annotation maps describing the entire Gene Ontology")
(description
@@ -523,12 +517,12 @@ information about the latest version of the Gene Ontologies.")
`((upstream-name . "Homo.sapiens")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)
- ("r-go-db" ,r-go-db)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
- ("r-organismdbi" ,r-organismdbi)
- ("r-annotationdbi" ,r-annotationdbi)))
+ (list r-genomicfeatures
+ r-go-db
+ r-org-hs-eg-db
+ r-txdb-hsapiens-ucsc-hg19-knowngene
+ r-organismdbi
+ r-annotationdbi))
(home-page "https://bioconductor.org/packages/Homo.sapiens/")
(synopsis "Annotation package for the Homo.sapiens object")
(description
@@ -550,13 +544,12 @@ several related annotation packages.")
(properties `((upstream-name . "Mus.musculus")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-go-db" ,r-go-db)
- ("r-org-mm-eg-db" ,r-org-mm-eg-db)
- ("r-organismdbi" ,r-organismdbi)
- ("r-txdb-mmusculus-ucsc-mm10-knowngene"
- ,r-txdb-mmusculus-ucsc-mm10-knowngene)))
+ (list r-annotationdbi
+ r-genomicfeatures
+ r-go-db
+ r-org-mm-eg-db
+ r-organismdbi
+ r-txdb-mmusculus-ucsc-mm10-knowngene))
(home-page "https://bioconductor.org/packages/Mus.musculus")
(synopsis "Annotation package for the Mus.musculus object")
(description
@@ -578,7 +571,7 @@ from several related annotation packages.")
`((upstream-name . "org.Ce.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
(synopsis "Genome wide annotation for Worm")
(description
@@ -600,7 +593,7 @@ annotations for the genome of the model worm Caenorhabditis elegans.")
`((upstream-name . "org.Dm.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
(synopsis "Genome wide annotation for Fly")
(description
@@ -622,7 +615,7 @@ annotations for the genome of the model fruit fly Drosophila melanogaster.")
`((upstream-name . "org.Dr.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
(synopsis "Annotation for Zebrafish")
(description
@@ -644,7 +637,7 @@ based on mapping using Entrez Gene identifiers.")
`((upstream-name . "org.Hs.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
(synopsis "Genome wide annotation for Human")
(description
@@ -666,7 +659,7 @@ on mapping using Entrez Gene identifiers.")
`((upstream-name . "org.Mm.eg.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
(synopsis "Genome wide annotation for Mouse")
(description
@@ -689,7 +682,7 @@ annotations for the genome of the model mouse Mus musculus.")
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
(synopsis "Full genome sequences for Homo sapiens")
@@ -713,7 +706,7 @@ by UCSC (hg19, February 2009) and stored in Biostrings objects.")
`((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)))
+ (list r-bsgenome))
(home-page
"https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
(synopsis "Full genome sequences for Homo sapiens")
@@ -737,7 +730,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
`((upstream-name . "EnsDb.Hsapiens.v75")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ensembldb" ,r-ensembldb)))
+ (list r-ensembldb))
(home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
(synopsis "Ensembl based annotation package")
(description
@@ -760,8 +753,7 @@ as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
`((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-genomicfeatures" ,r-genomicfeatures)))
+ (list r-annotationdbi r-genomicfeatures))
(home-page
"https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
(synopsis "Annotation package for TxDb object(s)")
@@ -785,7 +777,7 @@ exposing these as TxDb objects.")
`((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)))
+ (list r-genomicfeatures))
(home-page
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
(synopsis "Annotation package for human genome in TxDb format")
@@ -810,7 +802,7 @@ track. The database is exposed as a @code{TxDb} object.")
`((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)))
+ (list r-genomicfeatures))
(home-page
"https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
(synopsis "Annotation package for human genome in TxDb format")
@@ -835,8 +827,7 @@ track. The database is exposed as a @code{TxDb} object.")
`((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)
- ("r-annotationdbi" ,r-annotationdbi)))
+ (list r-genomicfeatures r-annotationdbi))
(home-page
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
(synopsis "Annotation package for mouse genome in TxDb format")
@@ -861,9 +852,7 @@ database is exposed as a @code{TxDb} object.")
`((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-annotationdbi" ,r-annotationdbi)))
+ (list r-bsgenome r-genomicfeatures r-annotationdbi))
(home-page
"https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
(synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
@@ -890,8 +879,7 @@ based on the knownGene track.")
`((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-genomicfeatures" ,r-genomicfeatures)))
+ (list r-annotationdbi r-genomicfeatures))
(home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
(synopsis "Annotation package for C elegans TxDb objects")
(description
@@ -914,11 +902,8 @@ by exposing these as TxDb objects.")
`((upstream-name . "FDb.InfiniumMethylation.hg19")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+ (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
+ r-txdb-hsapiens-ucsc-hg19-knowngene))
(home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
(synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
(description
@@ -942,7 +927,7 @@ annotations.")
`((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
(build-system r-build-system)
(propagated-inputs
- `(("r-minfi" ,r-minfi)))
+ (list r-minfi))
(home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
(synopsis "Manifest for Illumina's EPIC methylation arrays")
(description
@@ -963,7 +948,7 @@ annotations.")
`((upstream-name . "DO.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/DO.db/")
(synopsis "Annotation maps describing the entire Disease Ontology")
(description
@@ -985,7 +970,7 @@ Disease Ontology.")
(properties `((upstream-name . "PFAM.db")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://bioconductor.org/packages/PFAM.db")
(synopsis "Set of protein ID mappings for PFAM")
(description
@@ -1009,12 +994,12 @@ using data from public repositories.")
`((upstream-name . "phastCons100way.UCSC.hg19")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-genomicscores" ,r-genomicscores)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-bsgenome
+ r-genomeinfodb
+ r-genomicranges
+ r-genomicscores
+ r-iranges
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
(synopsis "UCSC phastCons conservation scores for hg19")
(description
@@ -1040,7 +1025,7 @@ species.")
`((upstream-name . "ABAData")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)))
+ (list r-annotationdbi))
(home-page "https://www.bioconductor.org/packages/ABAData/")
(synopsis "Gene expression in human brain regions from Allen Brain Atlas")
(description
@@ -1087,29 +1072,29 @@ All datasets are restricted to protein coding genes.")
"0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-aneufinderdata" ,r-aneufinderdata)
- ("r-ecp" ,r-ecp)
- ("r-foreach" ,r-foreach)
- ("r-doparallel" ,r-doparallel)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-bamsignals" ,r-bamsignals)
- ("r-dnacopy" ,r-dnacopy)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-ggplot2" ,r-ggplot2)
- ("r-reshape2" ,r-reshape2)
- ("r-ggdendro" ,r-ggdendro)
- ("r-ggrepel" ,r-ggrepel)
- ("r-reordercluster" ,r-reordercluster)
- ("r-mclust" ,r-mclust)
- ("r-cowplot" ,r-cowplot)))
+ (list r-knitr))
+ (propagated-inputs
+ (list r-genomicranges
+ r-aneufinderdata
+ r-ecp
+ r-foreach
+ r-doparallel
+ r-biocgenerics
+ r-s4vectors
+ r-genomeinfodb
+ r-iranges
+ r-rsamtools
+ r-bamsignals
+ r-dnacopy
+ r-biostrings
+ r-genomicalignments
+ r-ggplot2
+ r-reshape2
+ r-ggdendro
+ r-ggrepel
+ r-reordercluster
+ r-mclust
+ r-cowplot))
(home-page "https://bioconductor.org/packages/AneuFinder/")
(synopsis "Copy number variation analysis in single-cell-sequencing data")
(description "This package implements functions for copy number variant
@@ -1152,10 +1137,8 @@ from Illumina 450k methylation arrays.")
`((upstream-name . "biscuiteerData")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-curl" ,r-curl)
- ("r-experimenthub" ,r-experimenthub)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-annotationhub r-curl r-experimenthub))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/biscuiteerData")
(synopsis "Data package for Biscuiteer")
(description
@@ -1222,8 +1205,7 @@ GenomicRanges Bioconductor package.")
`((upstream-name . "geneLenDataBase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rtracklayer" ,r-rtracklayer)
- ("r-genomicfeatures" ,r-genomicfeatures)))
+ (list r-rtracklayer r-genomicfeatures))
(home-page "https://bioconductor.org/packages/geneLenDataBase/")
(synopsis "Lengths of mRNA transcripts for a number of genomes")
(description
@@ -1248,7 +1230,7 @@ genomes and gene ID formats, largely based on the UCSC table browser.")
;; make sense to build substitutes.
(arguments `(#:substitutable? #f))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Experimental data for use with the genomation package")
(description
@@ -1271,10 +1253,7 @@ downloaded from Encode.")
"0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocstyle" ,r-biocstyle)
- ("r-dexseq" ,r-dexseq)
- ("r-knitr" ,r-knitr)
- ("r-rmarkdown" ,r-rmarkdown)))
+ (list r-biocstyle r-dexseq r-knitr r-rmarkdown))
(home-page "https://www.bioconductor.org/packages/pasilla/")
(synopsis "Data package with per-exon and per-gene read counts")
(description "This package provides per-exon and per-gene read counts
@@ -1325,7 +1304,7 @@ resulting in a complete gene expression profile for each cell.")
(properties `((upstream-name . "ALL")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)))
+ (list r-biobase))
(home-page "https://bioconductor.org/packages/ALL")
(synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
(description
@@ -1350,7 +1329,7 @@ the form of an @code{exprSet} object.")
(properties `((upstream-name . "affydata")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)))
+ (list r-affy))
(home-page "https://bioconductor.org/packages/affydata/")
(synopsis "Affymetrix data for demonstration purposes")
(description
@@ -1400,12 +1379,12 @@ yeast are also included.")
`((upstream-name . "curatedTCGAData")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-experimenthub" ,r-experimenthub)
- ("r-hdf5array" ,r-hdf5array)
- ("r-multiassayexperiment" ,r-multiassayexperiment)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-annotationhub
+ r-experimenthub
+ r-hdf5array
+ r-multiassayexperiment
+ r-s4vectors
+ r-summarizedexperiment))
(home-page "https://bioconductor.org/packages/curatedTCGAData/")
(synopsis "Curated data from The Cancer Genome Atlas")
(description
@@ -1473,12 +1452,12 @@ packages.")
"0sb1h5qsk41c9xisq73agqh502wv6p2j1k45s32a4bkdynf696as"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-genomicranges" ,r-genomicranges)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rsamtools" ,r-rsamtools)))
+ (list r-s4vectors
+ r-iranges
+ r-genomicranges
+ r-genomicalignments
+ r-rtracklayer
+ r-rsamtools))
(home-page "https://bioconductor.org/packages/CoverageView/")
(synopsis "Coverage visualization package for R")
(description "This package provides a framework for the visualization of
@@ -1500,16 +1479,16 @@ how the coverage distributed across the genome.")
"0130hrlz2jabbshis1g11ndda8b8vlirzi7a004li3cgdghscxql"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-fastcluster" ,r-fastcluster)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gviz" ,r-gviz)
- ("r-plyr" ,r-plyr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biobase
+ r-biocgenerics
+ r-fastcluster
+ r-ggplot2
+ r-gviz
+ r-plyr
+ r-reshape2
+ r-rsqlite
+ r-rtracklayer
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/cummeRbund/")
(synopsis "Analyze Cufflinks high-throughput sequencing data")
(description "This package allows for persistent storage, access,
@@ -1560,12 +1539,12 @@ set analyses, and can deal with repeated or longitudinal data.")
"0a9k3f70jmd17kxf1zjmdzrfjs0dmwfad2zgz6wihxh5s1shc8qm"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-iranges" ,r-iranges)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
+ (list r-biostrings
+ r-dbi
+ r-iranges
+ r-rsqlite
+ r-s4vectors
+ r-xvector))
(home-page "https://www.bioconductor.org/packages/DECIPHER/")
(synopsis "Tools for deciphering and managing biological sequences")
(description "This package provides a toolset for deciphering and managing
@@ -1585,15 +1564,15 @@ biological sequences.")
(properties `((upstream-name . "deepSNV")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)
- ("r-vgam" ,r-vgam)))
+ (list r-biostrings
+ r-genomicranges
+ r-iranges
+ r-rhtslib
+ r-summarizedexperiment
+ r-variantannotation
+ r-vgam))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/gerstung-lab/deepSNV/")
(synopsis "Detection of subclonal SNVs in deep sequencing data")
(description
@@ -1622,13 +1601,10 @@ bases such as COSMIC.")
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-matrixgenerics" ,r-matrixgenerics)))
+ (list r-biocgenerics r-s4vectors r-iranges r-matrix
+ r-matrixgenerics))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/DelayedArray")
(synopsis "Delayed operations on array-like objects")
(description
@@ -1654,11 +1630,9 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns),
(properties `((upstream-name . "derfinderHelper")))
(build-system r-build-system)
(propagated-inputs
- `(("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-iranges r-matrix r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/leekgroup/derfinderHelper")
(synopsis "Helper for derfinder")
(description
@@ -1681,17 +1655,17 @@ calculation in parallel.")
(properties `((upstream-name . "DRIMSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-edger" ,r-edger)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-mass" ,r-mass)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-edger
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-limma
+ r-mass
+ r-reshape2
+ r-s4vectors))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/DRIMSeq")
(synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
(description
@@ -1716,15 +1690,15 @@ results.")
(properties `((upstream-name . "bluster")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-cluster" ,r-cluster)
- ("r-igraph" ,r-igraph)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocneighbors
+ r-biocparallel
+ r-cluster
+ r-igraph
+ r-matrix
+ r-rcpp
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/bluster")
(synopsis "Clustering algorithms for Bioconductor")
(description"This package wraps common clustering algorithms in an easily
@@ -1745,12 +1719,12 @@ and evaluate clustering results.")
"0cclk2pcb2mvsfxhw0zq3qlnfkblb1gqxnn7xypmlf0bm6hcvl4g"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-iranges" ,r-iranges)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-genomeinfodb" ,r-genomeinfodb)))
+ (list r-biobase
+ r-iranges
+ r-genomicranges
+ r-rcolorbrewer
+ r-rtracklayer
+ r-genomeinfodb))
(home-page "https://bioconductor.org/packages/IdeoViz/")
(synopsis "Plots data along a chromosomal ideogram")
(description "This package provides functions to plot data associated with
@@ -1771,8 +1745,7 @@ arbitrary genomic intervals along chromosomal ideogram.")
`((upstream-name . "IRanges")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics r-s4vectors))
(home-page "https://bioconductor.org/packages/IRanges")
(synopsis "Infrastructure for manipulating intervals on sequences")
(description
@@ -1799,37 +1772,37 @@ possible.")
(properties `((upstream-name . "IsoformSwitchAnalyzeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-dbi" ,r-dbi)
- ("r-dexseq" ,r-dexseq)
- ("r-dplyr" ,r-dplyr)
- ("r-drimseq" ,r-drimseq)
- ("r-edger" ,r-edger)
- ("r-futile-logger" ,r-futile-logger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-magrittr" ,r-magrittr)
- ("r-plyr" ,r-plyr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcurl" ,r-rcurl)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tximeta" ,r-tximeta)
- ("r-tximport" ,r-tximport)
- ("r-venndiagram" ,r-venndiagram)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-bsgenome
+ r-dbi
+ r-dexseq
+ r-dplyr
+ r-drimseq
+ r-edger
+ r-futile-logger
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-gridextra
+ r-iranges
+ r-limma
+ r-magrittr
+ r-plyr
+ r-rcolorbrewer
+ r-rcurl
+ r-readr
+ r-reshape2
+ r-rtracklayer
+ r-stringr
+ r-tibble
+ r-tximeta
+ r-tximport
+ r-venndiagram
+ r-xvector))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
(synopsis "Analyze alternative splicing in RNA-seq data")
(description
@@ -1853,11 +1826,7 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
(properties `((upstream-name . "AbsFilterGSEA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-deseq" ,r-deseq)
- ("r-limma" ,r-limma)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
(home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
(synopsis "Improved false positive control of gene-permuting with absolute filtering")
(description
@@ -1881,10 +1850,9 @@ absolute GSEA.")
(properties `((upstream-name . "BisqueRNA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-limsolve" ,r-limsolve)))
+ (list r-biobase r-limsolve))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://www.biorxiv.org/content/10.1101/669911v1")
(synopsis "Decomposition of bulk expression with single-cell sequencing")
(description "This package provides tools to accurately estimate cell type
@@ -1911,10 +1879,8 @@ relative abundances across samples.")
`((upstream-name . "deconstructSigs")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-reshape2" ,r-reshape2)))
+ (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
+ r-reshape2))
(home-page "https://github.com/raerose01/deconstructSigs")
(synopsis "Identifies signatures present in a tumor sample")
(description "This package takes sample information in the form of the
@@ -1938,25 +1904,25 @@ closely reconstructs the mutational profile.")
(properties `((upstream-name . "NMF")))
(build-system r-build-system)
(propagated-inputs
- `(("r-cluster" ,r-cluster)
- ("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-bigmemory" ,r-bigmemory) ; suggested
- ("r-synchronicity" ,r-synchronicity) ; suggested
- ("r-colorspace" ,r-colorspace)
- ("r-digest" ,r-digest)
- ("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridbase" ,r-gridbase)
- ("r-pkgmaker" ,r-pkgmaker)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-registry" ,r-registry)
- ("r-reshape2" ,r-reshape2)
- ("r-rngtools" ,r-rngtools)
- ("r-stringr" ,r-stringr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-cluster
+ r-biobase
+ r-biocmanager
+ r-bigmemory ; suggested
+ r-synchronicity ; suggested
+ r-colorspace
+ r-digest
+ r-doparallel
+ r-foreach
+ r-ggplot2
+ r-gridbase
+ r-pkgmaker
+ r-rcolorbrewer
+ r-registry
+ r-reshape2
+ r-rngtools
+ r-stringr))
+ (native-inputs
+ (list r-knitr))
(home-page "http://renozao.github.io/NMF")
(synopsis "Algorithms and framework for nonnegative matrix factorization")
(description
@@ -1981,14 +1947,14 @@ performing parallel computations on multicore machines.")
"0z66pyn2020h3x22xabkmnjxb20kbgblivvk7mqjk9134wvvf15a"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list r-affyio
+ r-biobase
+ r-biocgenerics
+ r-biocmanager
+ r-preprocesscore
+ r-zlibbioc))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://bioconductor.org/packages/affy")
(synopsis "Methods for affymetrix oligonucleotide arrays")
(description
@@ -2009,7 +1975,7 @@ analysis.")
"0kawlfff82ikrbrfyyy38zm5wj5xdri2ii9wgwilnq50z5qc6r21"))))
(properties `((upstream-name . "affycomp")))
(build-system r-build-system)
- (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (propagated-inputs (list r-biobase))
(home-page "https://bioconductor.org/packages/affycomp/")
(synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
(description
@@ -2032,9 +1998,7 @@ measures for Affymetrix Oligonucleotide Arrays.")
`((upstream-name . "AffyCompatible")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-rcurl" ,r-rcurl)
- ("r-xml" ,r-xml)))
+ (list r-biostrings r-rcurl r-xml))
(home-page "https://bioconductor.org/packages/AffyCompatible/")
(synopsis "Work with Affymetrix GeneChip files")
(description
@@ -2059,9 +2023,7 @@ Command Console} (AGCC)-compatible sample annotation files.")
(properties `((upstream-name . "affyContam")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-affydata" ,r-affydata)
- ("r-biobase" ,r-biobase)))
+ (list r-affy r-affydata r-biobase))
(home-page "https://bioconductor.org/packages/affyContam/")
(synopsis "Structured corruption of Affymetrix CEL file data")
(description
@@ -2084,27 +2046,27 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
(properties `((upstream-name . "affycoretools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-edger" ,r-edger)
- ("r-gcrma" ,r-gcrma)
- ("r-glimma" ,r-glimma)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gostats" ,r-gostats)
- ("r-gplots" ,r-gplots)
- ("r-hwriter" ,r-hwriter)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)
- ("r-oligoclasses" ,r-oligoclasses)
- ("r-reportingtools" ,r-reportingtools)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xtable" ,r-xtable)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-affy
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-dbi
+ r-edger
+ r-gcrma
+ r-glimma
+ r-ggplot2
+ r-gostats
+ r-gplots
+ r-hwriter
+ r-lattice
+ r-limma
+ r-oligoclasses
+ r-reportingtools
+ r-rsqlite
+ r-s4vectors
+ r-xtable))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/affycoretools/")
(synopsis "Functions for analyses with Affymetrix GeneChips")
(description
@@ -2125,9 +2087,9 @@ to streamline the more common analyses that a Biostatistician might see.")
"02lqdq8hcldkf9qbyhhllkm3smpqc51sn2d9gbkm74r96fx37lvm"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-zlibbioc" ,r-zlibbioc)))
+ (list r-zlibbioc))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(home-page "https://github.com/bmbolstad/affyio")
(synopsis "Tools for parsing Affymetrix data files")
(description
@@ -2177,13 +2139,13 @@ structure.")
"0p7q5hdk7003q72vg4hrgdzn463spybxhrkvcq3a6l6jkgy9sf84"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-httr" ,r-httr)
- ("r-xml" ,r-xml)
- ("r-xtable" ,r-xtable)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-dbi
+ r-httr
+ r-xml
+ r-xtable))
(home-page
"https://bioconductor.org/packages/annotate")
(synopsis "Annotation for microarrays")
@@ -2205,15 +2167,15 @@ microarrays.")
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-keggrest" ,r-keggrest)
- ("r-iranges" ,r-iranges)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biobase
+ r-biocgenerics
+ r-dbi
+ r-keggrest
+ r-iranges
+ r-rsqlite
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/AnnotationDbi")
(synopsis "Annotation database interface")
(description
@@ -2235,10 +2197,9 @@ annotation data packages using SQLite data storage.")
`((upstream-name . "AnnotationFilter")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-lazyeval" ,r-lazyeval)))
+ (list r-genomicranges r-lazyeval))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/Bioconductor/AnnotationFilter")
(synopsis "Facilities for filtering Bioconductor annotation resources")
(description
@@ -2262,16 +2223,16 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-dbi
+ r-rcurl
+ r-rsqlite
+ r-s4vectors
+ r-xml))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/AnnotationForge")
(synopsis "Code for building annotation database packages")
(description
@@ -2293,21 +2254,21 @@ databases. Packages produced are intended to be used with AnnotationDbi.")
(properties `((upstream-name . "AnnotationHub")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biocversion" ,r-biocversion)
- ("r-curl" ,r-curl)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-interactivedisplaybase" ,r-interactivedisplaybase)
- ("r-rappdirs" ,r-rappdirs)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biocfilecache
+ r-biocgenerics
+ r-biocmanager
+ r-biocversion
+ r-curl
+ r-dplyr
+ r-httr
+ r-interactivedisplaybase
+ r-rappdirs
+ r-rsqlite
+ r-s4vectors
+ r-yaml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/AnnotationHub")
(synopsis "Client to access AnnotationHub resources")
(description
@@ -2334,10 +2295,7 @@ by the user, helping with quick and reproducible access.")
(properties `((upstream-name . "aroma.light")))
(build-system r-build-system)
(propagated-inputs
- `(("r-matrixstats" ,r-matrixstats)
- ("r-r-methodss3" ,r-r-methodss3)
- ("r-r-oo" ,r-r-oo)
- ("r-r-utils" ,r-r-utils)))
+ (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
(home-page "https://github.com/HenrikBengtsson/aroma.light")
(synopsis "Methods for normalization and visualization of microarray data")
(description
@@ -2360,14 +2318,14 @@ classes.")
"03m3yaagplh7j4q5hp3cfcdqwsnh1pwrlla9cv3ajnfd83s8ncqv"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list r-biocgenerics
+ r-genomicranges
+ r-iranges
+ r-rcpp
+ r-rhtslib
+ r-zlibbioc))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/bamsignals")
(synopsis "Extract read count signals from bam files")
(description
@@ -2391,7 +2349,7 @@ paired-end data.")
`((upstream-name . "Biobase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)))
+ (list r-biocgenerics))
(home-page "https://bioconductor.org/packages/Biobase")
(synopsis "Base functions for Bioconductor")
(description
@@ -2413,17 +2371,17 @@ on Bioconductor or which replace R functions.")
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-digest" ,r-digest)
- ("r-httr" ,r-httr)
- ("r-progress" ,r-progress)
- ("r-rappdirs" ,r-rappdirs)
- ("r-stringr" ,r-stringr)
- ("r-xml" ,r-xml)
- ("r-xml2" ,r-xml2)))
+ (list r-annotationdbi
+ r-biocfilecache
+ r-digest
+ r-httr
+ r-progress
+ r-rappdirs
+ r-stringr
+ r-xml
+ r-xml2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/biomaRt")
(synopsis "Interface to BioMart databases")
(description
@@ -2479,11 +2437,9 @@ powerful online queries from gene annotation to database mining.")
(string-append
m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
(propagated-inputs
- `(("r-futile-logger" ,r-futile-logger)
- ("r-snow" ,r-snow)
- ("r-bh" ,r-bh)))
+ (list r-futile-logger r-snow r-bh))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocParallel")
(synopsis "Bioconductor facilities for parallel evaluation")
(description
@@ -2506,12 +2462,12 @@ objects.")
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-crayon" ,r-crayon)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
+ (list r-biocgenerics
+ r-crayon
+ r-genomeinfodb
+ r-iranges
+ r-s4vectors
+ r-xvector))
(home-page "https://bioconductor.org/packages/Biostrings")
(synopsis "String objects and algorithms for biological sequences")
(description
@@ -2534,25 +2490,25 @@ biological sequences or sets of sequences.")
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dichromat" ,r-dichromat)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
+ (list r-annotationdbi
+ r-annotationfilter
+ r-biocgenerics
+ r-biostrings
+ r-dichromat
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-hmisc
+ r-iranges
+ r-rcolorbrewer
+ r-rlang
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-summarizedexperiment
+ r-variantannotation))
(home-page "https://bioconductor.org/packages/biovizBase")
(synopsis "Basic graphic utilities for visualization of genomic data")
(description
@@ -2576,16 +2532,16 @@ effort and encourages consistency.")
`((upstream-name . "BSgenome")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
+ (list r-biocgenerics
+ r-biostrings
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrixstats
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-xvector))
(home-page "https://bioconductor.org/packages/BSgenome")
(synopsis "Infrastructure for Biostrings-based genome data packages")
(description
@@ -2607,16 +2563,16 @@ genome data packages and support for efficient SNP representation.")
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genefilter" ,r-genefilter)
- ("r-graph" ,r-graph)
- ("r-gseabase" ,r-gseabase)
- ("r-matrix" ,r-matrix)
- ("r-rbgl" ,r-rbgl)
- ("r-dbi" ,r-dbi)))
+ (list r-annotate
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-genefilter
+ r-graph
+ r-gseabase
+ r-matrix
+ r-rbgl
+ r-dbi))
(home-page "https://bioconductor.org/packages/Category")
(synopsis "Category analysis")
(description
@@ -2636,28 +2592,27 @@ analysis.")
"1nr5p1h9131rvbpnh2kizzx9q6f4ycq6rzxy1yqg2pczqcg7hy4x"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-boot" ,r-boot)
- ("r-enrichplot" ,r-enrichplot)
- ("r-iranges" ,r-iranges)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gplots" ,r-gplots)
- ("r-gtools" ,r-gtools)
- ("r-dplyr" ,r-dplyr)
- ("r-plotrix" ,r-plotrix)
- ("r-dplyr" ,r-dplyr)
- ("r-magrittr" ,r-magrittr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-txdb-hsapiens-ucsc-hg19-knowngene"
- ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+ (list r-knitr))
+ (propagated-inputs
+ (list r-annotationdbi
+ r-biocgenerics
+ r-boot
+ r-enrichplot
+ r-iranges
+ r-genomeinfodb
+ r-genomicranges
+ r-genomicfeatures
+ r-ggplot2
+ r-gplots
+ r-gtools
+ r-dplyr
+ r-plotrix
+ r-dplyr
+ r-magrittr
+ r-rcolorbrewer
+ r-rtracklayer
+ r-s4vectors
+ r-txdb-hsapiens-ucsc-hg19-knowngene))
(home-page "https://www.bioconductor.org/packages/ChIPseeker/")
(synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
(description "This package implements functions to retrieve the nearest
@@ -2684,12 +2639,12 @@ annotation, distance to TSS, and overlap of peaks or genes.")
"1jw209bfh1c22mqs9z44qx3pmca9m68rhxp0p9bvbmqsnqwrndi6"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shortread" ,r-shortread)))
+ (list r-biocgenerics
+ r-genomicranges
+ r-iranges
+ r-lattice
+ r-s4vectors
+ r-shortread))
(home-page "https://bioconductor.org/packages/chipseq")
(synopsis "Package for analyzing ChIPseq data")
(description
@@ -2712,20 +2667,20 @@ experiments.")
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
(propagated-inputs
- `(("r-circlize" ,r-circlize)
- ("r-clue" ,r-clue)
- ("r-colorspace" ,r-colorspace)
- ("r-digest" ,r-digest)
- ("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-getoptlong" ,r-getoptlong)
- ("r-globaloptions" ,r-globaloptions)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-png" ,r-png)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-circlize
+ r-clue
+ r-colorspace
+ r-digest
+ r-doparallel
+ r-foreach
+ r-getoptlong
+ r-globaloptions
+ r-iranges
+ r-matrixstats
+ r-png
+ r-rcolorbrewer))
+ (native-inputs
+ (list r-knitr))
(home-page
"https://github.com/jokergoo/ComplexHeatmap")
(synopsis "Making Complex Heatmaps")
@@ -2750,20 +2705,20 @@ self-defined annotation graphics.")
(properties `((upstream-name . "CopywriteR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-chipseq" ,r-chipseq)
- ("r-copyhelper" ,r-copyhelper)
- ("r-data-table" ,r-data-table)
- ("r-dnacopy" ,r-dnacopy)
- ("r-futile-logger" ,r-futile-logger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocparallel
+ r-chipseq
+ r-copyhelper
+ r-data-table
+ r-dnacopy
+ r-futile-logger
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-matrixstats
+ r-rsamtools
+ r-s4vectors))
(home-page "https://github.com/PeeperLab/CopywriteR")
(synopsis "Copy number information from targeted sequencing")
(description
@@ -2790,14 +2745,14 @@ number detection tools.")
(properties `((upstream-name . "DESeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-lattice" ,r-lattice)
- ("r-locfit" ,r-locfit)
- ("r-mass" ,r-mass)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-biobase
+ r-biocgenerics
+ r-genefilter
+ r-geneplotter
+ r-lattice
+ r-locfit
+ r-mass
+ r-rcolorbrewer))
(home-page "https://www-huber.embl.de/users/anders/DESeq/")
(synopsis "Differential gene expression analysis")
(description
@@ -2821,21 +2776,21 @@ distribution.")
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-locfit" ,r-locfit)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-genefilter
+ r-geneplotter
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-locfit
+ r-rcpp
+ r-rcpparmadillo
+ r-s4vectors
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/DESeq2")
(synopsis "Differential gene expression analysis")
(description
@@ -2859,25 +2814,25 @@ distribution.")
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biomart" ,r-biomart)
- ("r-deseq2" ,r-deseq2)
- ("r-genefilter" ,r-genefilter)
- ("r-geneplotter" ,r-geneplotter)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-statmod" ,r-statmod)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biomart
+ r-deseq2
+ r-genefilter
+ r-geneplotter
+ r-genomicranges
+ r-hwriter
+ r-iranges
+ r-rcolorbrewer
+ r-rsamtools
+ r-s4vectors
+ r-statmod
+ r-stringr
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/DEXSeq")
(synopsis "Inference of differential exon usage in RNA-Seq")
(description
@@ -2905,11 +2860,9 @@ exploration of the results.")
`((upstream-name . "DirichletMultinomial")))
(build-system r-build-system)
(inputs
- `(("gsl" ,gsl)))
+ (list gsl))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics r-iranges r-s4vectors))
(home-page "https://bioconductor.org/packages/DirichletMultinomial")
(synopsis "Dirichlet-Multinomial mixture models for microbiome data")
(description
@@ -2933,20 +2886,20 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-aroma-light" ,r-aroma-light)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-shortread" ,r-shortread)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-aroma-light
+ r-biobase
+ r-biocgenerics
+ r-biocmanager
+ r-biomart
+ r-biostrings
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rsamtools
+ r-shortread))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/drisso/EDASeq")
(synopsis "Exploratory data analysis and normalization for RNA-Seq")
(description
@@ -2972,10 +2925,7 @@ global-scaling and full-quantile normalization.")
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-limma" ,r-limma)
- ("r-locfit" ,r-locfit)
- ("r-rcpp" ,r-rcpp)
- ("r-statmod" ,r-statmod))) ;for estimateDisp
+ (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp
(home-page "http://bioinf.wehi.edu.au/edgeR")
(synopsis "EdgeR does empirical analysis of digital gene expression data")
(description "This package can do differential expression analysis of
@@ -3000,24 +2950,24 @@ CAGE.")
"0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-curl" ,r-curl)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationfilter
+ r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-curl
+ r-dbi
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-protgenerics
+ r-rsamtools
+ r-rsqlite
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/jotsetung/ensembldb")
(synopsis "Utilities to create and use Ensembl-based annotation databases")
(description
@@ -3045,11 +2995,8 @@ chromosome region or transcript models of lincRNA genes.")
"1ds0hhc41nhfj3lmvld8nk2p547wd80b3yq7fjlf3dl3wfaxzy80"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biobase r-biocgenerics r-genomicranges r-iranges
+ r-s4vectors))
(home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
(synopsis "Fast segmentation algorithm for genetic sequencing data")
(description
@@ -3075,10 +3022,7 @@ microarrays or GRanges for sequencing data.")
"1spndmvl8wlz3z3wsvzi0fg9nzk81xi8c220pg2rf81j9181nkar"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-keggrest" ,r-keggrest)))
+ (list r-annotationdbi r-go-db r-graph r-keggrest))
(home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
"articles/10.1186/1471-2105-10-161"))
(synopsis "Generally applicable gene-set enrichment for pathway analysis")
@@ -3106,14 +3050,10 @@ analysis using other methods.")
"05ba33m99dg414lasn36mjmkd9lvrxgpamy1qj2zvi31i9vkq6y2"))))
(build-system r-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
- ("r-knitr" ,r-knitr)))
+ (list gfortran r-knitr))
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-survival" ,r-survival)))
+ (list r-annotate r-annotationdbi r-biobase r-biocgenerics
+ r-survival))
(home-page "https://bioconductor.org/packages/genefilter")
(synopsis "Filter genes from high-throughput experiments")
(description
@@ -3133,8 +3073,7 @@ high-throughput sequencing experiments.")
"18l5dc4xcy1xa2h3sfw92w9rq9v0mnclamjxmzs5fqi469y5mwmm"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-gplots" ,r-gplots)))
+ (list r-rcolorbrewer r-gplots))
(home-page "https://www.bioconductor.org/packages/GeneOverlap/")
(synopsis "Test and visualize gene overlaps")
(description "This package can be used to test two sets of gene lists
@@ -3153,28 +3092,28 @@ and visualize the results.")
"0ynwsrlnp98iyz4bl2s7plin0k9iy9zix4jy4v38lcqg6n4iz00j"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-data-table" ,r-data-table)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridbase" ,r-gridbase)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-plotrix" ,r-plotrix)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqpattern" ,r-seqpattern)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biostrings
+ r-bsgenome
+ r-data-table
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-gridbase
+ r-impute
+ r-iranges
+ r-matrixstats
+ r-plotrix
+ r-plyr
+ r-rcpp
+ r-readr
+ r-reshape2
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-seqpattern))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioinformatics.mdc-berlin.de/genomation/")
(synopsis "Summary, annotation and visualization of genomic data")
(description
@@ -3202,13 +3141,10 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.")
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomeinfodbdata" ,r-genomeinfodbdata)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GenomeInfoDb")
(synopsis "Utilities for manipulating chromosome identifiers")
(description
@@ -3232,15 +3168,15 @@ names in their natural, rather than lexicographic, order.")
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-rsamtools
+ r-s4vectors
+ r-summarizedexperiment))
(home-page "https://bioconductor.org/packages/GenomicAlignments")
(synopsis "Representation and manipulation of short genomic alignments")
(description
@@ -3265,23 +3201,23 @@ alignments.")
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocio" ,r-biocio)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocio
+ r-biomart
+ r-biostrings
+ r-dbi
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-rcurl
+ r-rsqlite
+ r-rtracklayer
+ r-s4vectors
+ r-xvector))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GenomicFeatures")
(synopsis "Tools for working with transcript centric annotations")
(description
@@ -3309,18 +3245,18 @@ extracting the desired features in a convenient format.")
(properties `((upstream-name . "GenomicFiles")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-matrixgenerics
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-summarizedexperiment
+ r-variantannotation))
(home-page "https://bioconductor.org/packages/GenomicFiles")
(synopsis "Distributed computing by file or by range")
(description
@@ -3343,13 +3279,9 @@ provide added flexibility for data combination and manipulation.")
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
+ (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GenomicRanges")
(synopsis "Representation and manipulation of genomic intervals")
(description
@@ -3374,15 +3306,15 @@ manipulating genomic intervals and variables defined along a genome.")
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationforge" ,r-annotationforge)
- ("r-biobase" ,r-biobase)
- ("r-category" ,r-category)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rbgl" ,r-rbgl)))
+ (list r-annotate
+ r-annotationdbi
+ r-annotationforge
+ r-biobase
+ r-category
+ r-go-db
+ r-graph
+ r-rgraphviz
+ r-rbgl))
(home-page "https://bioconductor.org/packages/GOstats")
(synopsis "Tools for manipulating GO and microarrays")
(description
@@ -3405,14 +3337,14 @@ testing and other simple calculations.")
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-graph" ,r-graph)
- ("r-xml" ,r-xml)))
+ (list r-annotate
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-graph
+ r-xml))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GSEABase")
(synopsis "Gene set enrichment data structures and methods")
(description
@@ -3433,7 +3365,7 @@ Enrichment Analysis} (GSEA).")
"1inajapdhjxg0vwhsdnhfq22h3fv7ad7m1lv58y5v41p59av1w76"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
(description "This package provides a simple interface to and data from
@@ -3457,12 +3389,10 @@ the Human Protein Atlas project.")
;; which makes R abort the build.
(arguments '(#:configure-flags '("--no-staged-install")))
(propagated-inputs
- `(("curl" ,curl)
- ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list curl zlib ; packages using rhtslib need to link with zlib
+ r-zlibbioc))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
+ (list pkg-config r-knitr))
(home-page "https://github.com/nhayden/Rhtslib")
(synopsis "High-throughput sequencing library as an R package")
(description
@@ -3482,7 +3412,7 @@ of other R packages who wish to make use of HTSlib.")
(base32
"0k6dil8ljgp5qr87m7hxli4igb36fbxiwczaqc5pi8mlfh70fqj5"))))
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/impute")
(synopsis "Imputation for microarray data")
@@ -3506,11 +3436,9 @@ microarray data, using nearest neighbor averaging.")
`((upstream-name . "interactiveDisplayBase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-dt" ,r-dt)
- ("r-shiny" ,r-shiny)))
+ (list r-biocgenerics r-dt r-shiny))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/interactiveDisplayBase")
(synopsis "Base package for web displays of Bioconductor objects")
(description
@@ -3532,11 +3460,9 @@ Shiny-based display methods for Bioconductor objects.")
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-httr" ,r-httr)
- ("r-png" ,r-png)))
+ (list r-biostrings r-httr r-png))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/KEGGREST")
(synopsis "Client-side REST access to KEGG")
(description
@@ -3576,27 +3502,27 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-emdbook" ,r-emdbook)
- ("r-fastseg" ,r-fastseg)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-limma" ,r-limma)
- ("r-mclust" ,r-mclust)
- ("r-mgcv" ,r-mgcv)
- ("r-qvalue" ,r-qvalue)
- ("r-r-utils" ,r-r-utils)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
+ (list r-data-table
+ r-emdbook
+ r-fastseg
+ r-genomeinfodb
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-kernsmooth
+ r-limma
+ r-mclust
+ r-mgcv
+ r-qvalue
+ r-r-utils
+ r-rcpp
+ r-rhtslib
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-zlibbioc))
+ (native-inputs
+ (list r-knitr)) ; for vignettes
(home-page "https://github.com/al2na/methylKit")
(synopsis
"DNA methylation analysis from high-throughput bisulfite sequencing results")
@@ -3624,12 +3550,12 @@ TAB-Seq.")
(properties `((upstream-name . "motifRG")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-iranges" ,r-iranges)
- ("r-seqlogo" ,r-seqlogo)
- ("r-xvector" ,r-xvector)))
+ (list r-biostrings
+ r-bsgenome
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-iranges
+ r-seqlogo
+ r-xvector))
(home-page "https://bioconductor.org/packages/motifRG")
(synopsis "Discover motifs in high throughput sequencing data")
(description
@@ -3650,7 +3576,7 @@ throughput genetic sequencing data sets using regression methods.")
"1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
("r-biostrings" ,r-biostrings)
@@ -3697,30 +3623,30 @@ in SNV base substitution data.")
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-digest" ,r-digest)
- ("r-ggplot2" ,r-ggplot2)
- ("r-impute" ,r-impute)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-maldiquant" ,r-maldiquant)
- ("r-mass" ,r-mass)
- ("r-mscoreutils" ,r-mscoreutils)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-pcamethods" ,r-pcamethods)
- ("r-plyr" ,r-plyr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-vsn" ,r-vsn)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-affy
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-digest
+ r-ggplot2
+ r-impute
+ r-iranges
+ r-lattice
+ r-maldiquant
+ r-mass
+ r-mscoreutils
+ r-mzid
+ r-mzr
+ r-pcamethods
+ r-plyr
+ r-protgenerics
+ r-rcpp
+ r-s4vectors
+ r-scales
+ r-vsn
+ r-xml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/lgatto/MSnbase")
(synopsis "Base functions and classes for MS-based proteomics")
(description
@@ -3747,32 +3673,32 @@ of mass spectrometry based proteomics data.")
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocstyle" ,r-biocstyle)
- ("r-biostrings" ,r-biostrings)
- ("r-data-table" ,r-data-table)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iterators" ,r-iterators)
- ("r-msnbase" ,r-msnbase)
- ("r-msmstests" ,r-msmstests)
- ("r-mzid" ,r-mzid)
- ("r-mzr" ,r-mzr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-purrr" ,r-purrr)
- ("r-r-cache" ,r-r-cache)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-runit" ,r-runit)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-xtable" ,r-xtable)))
+ (list r-annotationdbi
+ r-annotationhub
+ r-biobase
+ r-biocgenerics
+ r-biocstyle
+ r-biostrings
+ r-data-table
+ r-doparallel
+ r-dplyr
+ r-foreach
+ r-ggplot2
+ r-iterators
+ r-msnbase
+ r-msmstests
+ r-mzid
+ r-mzr
+ r-protgenerics
+ r-purrr
+ r-r-cache
+ r-rcpp
+ r-reshape2
+ r-rlang
+ r-runit
+ r-stringr
+ r-tibble
+ r-xtable))
(home-page "https://bioconductor.org/packages/MSnID")
(synopsis "Utilities for LC-MSn proteomics identifications")
(description
@@ -3799,14 +3725,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(properties `((upstream-name . "mzID")))
(build-system r-build-system)
(propagated-inputs
- `(("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-iterators" ,r-iterators)
- ("r-plyr" ,r-plyr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-xml" ,r-xml)))
+ (list r-doparallel
+ r-foreach
+ r-iterators
+ r-plyr
+ r-protgenerics
+ r-xml))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/mzID")
(synopsis "Parser for mzIdentML files")
(description
@@ -3848,20 +3774,20 @@ specific parser.")
-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
#t)))))
(inputs
- `(;; Our default boost package won't work here, unfortunately, even with
- ;; mzR version 2.28.0.
- ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
- ("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-ncdf4" ,r-ncdf4)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rcpp" ,r-rcpp)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list ;; Our default boost package won't work here, unfortunately, even with
+ ;; mzR version 2.28.0.
+ boost-for-mysql ; use this instead of the bundled boost sources
+ zlib))
+ (propagated-inputs
+ (list r-biobase
+ r-biocgenerics
+ r-ncdf4
+ r-protgenerics
+ r-rcpp
+ r-rhdf5lib
+ r-zlibbioc))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/sneumann/mzR/")
(synopsis "Parser for mass spectrometry data files")
(description
@@ -3887,17 +3813,17 @@ previously been used in XCMS.")
(properties `((upstream-name . "OrganismDbi")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-dbi" ,r-dbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-graph" ,r-graph)
- ("r-iranges" ,r-iranges)
- ("r-rbgl" ,r-rbgl)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocmanager
+ r-dbi
+ r-genomicfeatures
+ r-genomicranges
+ r-graph
+ r-iranges
+ r-rbgl
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/OrganismDbi")
(synopsis "Software to enable the smooth interfacing of database packages")
(description "The package enables a simple unified interface to several
@@ -3919,10 +3845,7 @@ the fact that each of these packages implements a select methods.")
(properties `((upstream-name . "pcaMethods")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-mass" ,r-mass)
- ("r-rcpp" ,r-rcpp)))
+ (list r-biobase r-biocgenerics r-mass r-rcpp))
(home-page "https://github.com/hredestig/pcamethods")
(synopsis "Collection of PCA methods")
(description
@@ -3969,8 +3892,7 @@ proteomics packages.")
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-graph" ,r-graph)))
+ (list r-bh r-graph))
(home-page "https://www.bioconductor.org/packages/RBGL")
(synopsis "Interface to the Boost graph library")
(description
@@ -3991,35 +3913,35 @@ the graph algorithms contained in the Boost library.")
(properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-cowplot" ,r-cowplot)
- ("r-data-table" ,r-data-table)
- ("r-dt" ,r-dt)
- ("r-genomation" ,r-genomation)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggseqlogo" ,r-ggseqlogo)
- ("r-gprofiler2" ,r-gprofiler2)
- ("r-iranges" ,r-iranges)
- ("r-knitr" ,r-knitr)
- ("r-pbapply" ,r-pbapply)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plotly" ,r-plotly)
- ("r-plotrix" ,r-plotrix)
- ("r-proxy" ,r-proxy)
- ("r-ranger" ,r-ranger)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-s4vectors" ,r-s4vectors)
- ("pandoc" ,pandoc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-bsgenome
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-cowplot
+ r-data-table
+ r-dt
+ r-genomation
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-ggseqlogo
+ r-gprofiler2
+ r-iranges
+ r-knitr
+ r-pbapply
+ r-pheatmap
+ r-plotly
+ r-plotrix
+ r-proxy
+ r-ranger
+ r-rsqlite
+ r-rtracklayer
+ r-rmarkdown
+ r-s4vectors
+ pandoc))
+ (native-inputs
+ (list r-knitr))
(synopsis "RNA-centric annotation system")
(description
"RCAS aims to be a standalone RNA-centric annotation system that provides
@@ -4042,16 +3964,16 @@ library implementing most of the pipeline's features.")
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-memoise" ,r-memoise)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-memoise
+ r-rtracklayer
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/regioneR/")
(synopsis "Association analysis of genomic regions")
(description "This package offers a statistical framework based on
@@ -4074,27 +3996,27 @@ region sets and other genomic features.")
`((upstream-name . "ReportingTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-category" ,r-category)
- ("r-deseq2" ,r-deseq2)
- ("r-edger" ,r-edger)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gostats" ,r-gostats)
- ("r-gseabase" ,r-gseabase)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-knitr" ,r-knitr)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)
- ("r-pfam-db" ,r-pfam-db)
- ("r-r-utils" ,r-r-utils)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotate
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-category
+ r-deseq2
+ r-edger
+ r-ggbio
+ r-ggplot2
+ r-gostats
+ r-gseabase
+ r-hwriter
+ r-iranges
+ r-knitr
+ r-lattice
+ r-limma
+ r-pfam-db
+ r-r-utils
+ r-xml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ReportingTools/")
(synopsis "Tools for making reports in various formats")
(description
@@ -4121,10 +4043,9 @@ browser.")
"13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-rhdf5filters" ,r-rhdf5filters)
- ("r-rhdf5lib" ,r-rhdf5lib)))
+ (list r-rhdf5filters r-rhdf5lib))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/rhdf5")
(synopsis "HDF5 interface to R")
(description
@@ -4151,11 +4072,11 @@ the available RAM.")
(properties `((upstream-name . "rhdf5filters")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rhdf5lib" ,r-rhdf5lib)))
+ (list r-rhdf5lib))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/grimbough/rhdf5filters")
(synopsis "HDF5 compression filters")
(description
@@ -4186,16 +4107,16 @@ HDF5 datasets.")
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") "")))))))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bitops" ,r-bitops)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bitops
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-rhtslib
+ r-s4vectors
+ r-xvector))
(home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
(synopsis "Interface to samtools, bcftools, and tabix")
(description
@@ -4221,11 +4142,7 @@ tab-delimited (tabix) files.")
(properties `((upstream-name . "restfulr")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcurl" ,r-rcurl)
- ("r-rjson" ,r-rjson)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)
- ("r-yaml" ,r-yaml)))
+ (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
(home-page "https://cran.r-project.org/package=restfulr")
(synopsis "R interface to RESTful web services")
(description
@@ -4253,24 +4170,24 @@ tab-delimited (tabix) files.")
(substitute* "NAMESPACE"
(("import\\(zlibbioc\\)") "")))))))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocio" ,r-biocio)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-restfulr" ,r-restfulr)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list zlib))
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biocio
+ r-biostrings
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-rcurl
+ r-restfulr
+ r-rsamtools
+ r-s4vectors
+ r-xml
+ r-xvector
+ r-zlibbioc))
(home-page "https://bioconductor.org/packages/rtracklayer")
(synopsis "R interface to genome browsers and their annotation tracks")
(description
@@ -4296,13 +4213,13 @@ as well as query and modify the browser state, such as the current viewport.")
(properties `((upstream-name . "samr")))
(build-system r-build-system)
(propagated-inputs
- `(("r-gsa" ,r-gsa)
- ("r-impute" ,r-impute)
- ("r-matrixstats" ,r-matrixstats)
- ("r-openxlsx" ,r-openxlsx)
- ("r-shiny" ,r-shiny)
- ("r-shinyfiles" ,r-shinyfiles)))
- (native-inputs `(("gfortran" ,gfortran)))
+ (list r-gsa
+ r-impute
+ r-matrixstats
+ r-openxlsx
+ r-shiny
+ r-shinyfiles))
+ (native-inputs (list gfortran))
(home-page "https://statweb.stanford.edu/~tibs/SAM/")
(synopsis "Significance analysis of Microarrays")
(description
@@ -4324,23 +4241,23 @@ differential expression analysis, RNAseq data and related problems.")
(properties `((upstream-name . "scDblFinder")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-bluster" ,r-bluster)
- ("r-delayedarray" ,r-delayedarray)
- ("r-igraph" ,r-igraph)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scater" ,r-scater)
- ("r-scran" ,r-scran)
- ("r-scuttle" ,r-scuttle)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-xgboost" ,r-xgboost)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biocneighbors
+ r-biocparallel
+ r-biocsingular
+ r-bluster
+ r-delayedarray
+ r-igraph
+ r-mass
+ r-matrix
+ r-s4vectors
+ r-scater
+ r-scran
+ r-scuttle
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-xgboost))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/plger/scDblFinder")
(synopsis "Detect multiplets in single-cell RNA sequencing data")
(description
@@ -4365,7 +4282,7 @@ comprehensive scDblFinder method.")
(properties `((upstream-name . "seqLogo")))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/seqLogo")
(synopsis "Sequence logos for DNA sequence alignments")
(description
@@ -4388,11 +4305,7 @@ Stephens (1990).")
`((upstream-name . "seqPattern")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-plotrix" ,r-plotrix)))
+ (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
(home-page "https://bioconductor.org/packages/seqPattern")
(synopsis "Visualising oligonucleotide patterns and motif occurrences")
(description
@@ -4415,24 +4328,24 @@ reference point and sorted by a user defined feature.")
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rhtslib" ,r-rhtslib)
- ("r-hwriter" ,r-hwriter)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list zlib))
+ (propagated-inputs
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-rhtslib
+ r-hwriter
+ r-iranges
+ r-lattice
+ r-latticeextra
+ r-rsamtools
+ r-s4vectors
+ r-xvector
+ r-zlibbioc))
(home-page "https://bioconductor.org/packages/ShortRead")
(synopsis "FASTQ input and manipulation tools")
(description
@@ -4459,22 +4372,22 @@ ungapped alignment formats.")
`((upstream-name . "simplifyEnrichment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-circlize" ,r-circlize)
- ("r-clue" ,r-clue)
- ("r-cluster" ,r-cluster)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-digest" ,r-digest)
- ("r-getoptlong" ,r-getoptlong)
- ("r-go-db" ,r-go-db)
- ("r-gosemsim" ,r-gosemsim)
- ("r-matrix" ,r-matrix)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-proxyc" ,r-proxyc)
- ("r-slam" ,r-slam)
- ("r-tm" ,r-tm)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biocgenerics
+ r-circlize
+ r-clue
+ r-cluster
+ r-complexheatmap
+ r-digest
+ r-getoptlong
+ r-go-db
+ r-gosemsim
+ r-matrix
+ r-org-hs-eg-db
+ r-proxyc
+ r-slam
+ r-tm))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/jokergoo/simplifyEnrichment")
(synopsis "Simplify functional enrichment results")
(description "This package provides a new clustering algorithm, binary
@@ -4498,12 +4411,9 @@ and comparing the clusterings.")
`((upstream-name . "TrajectoryUtils")))
(build-system r-build-system)
(propagated-inputs
- `(("r-igraph" ,r-igraph)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/TrajectoryUtils")
(synopsis "Single-cell trajectory analysis utilities")
(description
@@ -4525,15 +4435,15 @@ structures to hold pseudotime inference results.")
"081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-igraph" ,r-igraph)
- ("r-matrixstats" ,r-matrixstats)
- ("r-princurve" ,r-princurve)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-trajectoryutils" ,r-trajectoryutils)))
+ (list r-igraph
+ r-matrixstats
+ r-princurve
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-trajectoryutils))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/slingshot")
(synopsis "Tools for ordering single-cell sequencing")
(description "This package provides functions for inferring continuous,
@@ -4558,15 +4468,15 @@ graph construction.")
(properties `((upstream-name . "STRINGdb")))
(build-system r-build-system)
(propagated-inputs
- `(("r-gplots" ,r-gplots)
- ("r-hash" ,r-hash)
- ("r-igraph" ,r-igraph)
- ("r-plotrix" ,r-plotrix)
- ("r-plyr" ,r-plyr)
- ("r-png" ,r-png)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcurl" ,r-rcurl)
- ("r-sqldf" ,r-sqldf)))
+ (list r-gplots
+ r-hash
+ r-igraph
+ r-plotrix
+ r-plyr
+ r-png
+ r-rcolorbrewer
+ r-rcurl
+ r-sqldf))
(home-page "https://git.bioconductor.org/packages/STRINGdb")
(synopsis "Search tool for the retrieval of interacting proteins database")
(description
@@ -4590,22 +4500,22 @@ that integrates the various evidences.")
(base32 "1pw7d39944dwk5gw6q7igcn866zpqwz01ljaha2ih5dfvmhxka8n"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rlang" ,r-rlang)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-assertthat
+ r-biocgenerics
+ r-biostrings
+ r-dplyr
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rlang
+ r-rtracklayer
+ r-s4vectors
+ r-stringr
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
(synopsis "R package designed to simplify structural variant analysis")
(description
@@ -4629,17 +4539,17 @@ involving two separate genomic loci encoded as GRanges objects.")
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biobase
+ r-biocgenerics
+ r-delayedarray
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-matrixgenerics
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/SummarizedExperiment")
(synopsis "Container for representing genomic ranges by sample")
(description
@@ -4662,12 +4572,12 @@ samples.")
"0clzid9di2qfgc5bvnqx312k3inj1lc599ckqkllvr894wxb7mdj"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-edger" ,r-edger)
- ("r-genefilter" ,r-genefilter)
- ("r-mgcv" ,r-mgcv)
- ("r-biocparallel" ,r-biocparallel)
- ("r-matrixstats" ,r-matrixstats)
- ("r-limma" ,r-limma)))
+ (list r-edger
+ r-genefilter
+ r-mgcv
+ r-biocparallel
+ r-matrixstats
+ r-limma))
(home-page "https://bioconductor.org/packages/sva")
(synopsis "Surrogate variable analysis")
(description
@@ -4694,21 +4604,21 @@ unmodeled, or latent sources of noise.")
(properties `((upstream-name . "systemPipeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-crayon" ,r-crayon)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-magrittr" ,r-magrittr)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shortread" ,r-shortread)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-crayon
+ r-genomicranges
+ r-ggplot2
+ r-htmlwidgets
+ r-magrittr
+ r-rsamtools
+ r-s4vectors
+ r-shortread
+ r-stringr
+ r-summarizedexperiment
+ r-yaml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/tgirke/systemPipeR")
(synopsis "Next generation sequencing workflow and reporting environment")
(description
@@ -4737,15 +4647,15 @@ annotation infrastructure.")
`((upstream-name . "topGO")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dbi" ,r-dbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-go-db" ,r-go-db)
- ("r-graph" ,r-graph)
- ("r-lattice" ,r-lattice)
- ("r-matrixstats" ,r-matrixstats)
- ("r-sparsem" ,r-sparsem)))
+ (list r-annotationdbi
+ r-dbi
+ r-biobase
+ r-biocgenerics
+ r-go-db
+ r-graph
+ r-lattice
+ r-matrixstats
+ r-sparsem))
(home-page "https://bioconductor.org/packages/topGO")
(synopsis "Enrichment analysis for gene ontology")
(description
@@ -4768,7 +4678,7 @@ dependencies between GO terms can be implemented and applied.")
"0w6pr7s9j8l4fpn3przbfrsyxvzxc3ficgsychvhq3bami9np8g4"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/tximport")
(synopsis "Import and summarize transcript-level estimates for gene-level analysis")
(description
@@ -4793,24 +4703,24 @@ of gene-level counts.")
(properties
`((upstream-name . "VariantAnnotation")))
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-bsgenome
+ r-dbi
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-matrixgenerics
+ r-summarizedexperiment
+ r-rhtslib
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-xvector
+ r-zlibbioc))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/VariantAnnotation")
(synopsis "Package for annotation of genetic variants")
@@ -4831,13 +4741,9 @@ coding changes and predict coding outcomes.")
"03p2wdjbjnrn1ddyz0fbn04mdxpsmv83qhh3apj6azshl0bs1j2x"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-ggplot2" ,r-ggplot2)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)))
+ (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
(native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
+ (list r-knitr)) ; for vignettes
(home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
(synopsis "Variance stabilization and calibration for microarray data")
(description
@@ -4867,14 +4773,14 @@ and specific in detecting differential transcription.")
(properties `((upstream-name . "XINA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-alluvial" ,r-alluvial)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-igraph" ,r-igraph)
- ("r-mclust" ,r-mclust)
- ("r-plyr" ,r-plyr)
- ("r-stringdb" ,r-stringdb)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-alluvial
+ r-ggplot2
+ r-gridextra
+ r-igraph
+ r-mclust
+ r-plyr
+ r-stringdb))
+ (native-inputs (list r-knitr))
(home-page "https://git.bioconductor.org/packages/XINA")
(synopsis "Identifying proteins that exhibit similar patterns")
(description
@@ -4941,11 +4847,9 @@ describing each of the graphs.")
(("import\\(zlibbioc\\)") ""))
#t)))))
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics r-iranges r-s4vectors))
(home-page "https://bioconductor.org/packages/XVector")
(synopsis "Representation and manpulation of external sequences")
(description
@@ -4985,15 +4889,15 @@ libraries for systems that do not have these available via other means.")
(properties `((upstream-name . "zellkonverter")))
(build-system r-build-system)
(propagated-inputs
- `(("r-basilisk" ,r-basilisk)
- ("r-cli" ,r-cli)
- ("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)
- ("r-reticulate" ,r-reticulate)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-basilisk
+ r-cli
+ r-delayedarray
+ r-matrix
+ r-reticulate
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/theislab/zellkonverter")
(synopsis "Conversion between AnnData and single-cell experiments objects")
(description
@@ -5017,12 +4921,12 @@ saving AnnData objects to disk.")
"1b7ngp9l00vrymx3d3nsda546s7p4ifr90idn3x2v4ilf38rfhp8"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-lattice" ,r-lattice)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-annotate
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-lattice
+ r-rcolorbrewer))
(home-page "https://bioconductor.org/packages/geneplotter")
(synopsis "Graphics functions for genomic data")
(description
@@ -5043,19 +4947,19 @@ saving AnnData objects to disk.")
(properties `((upstream-name . "oligoClasses")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-ff" ,r-ff)
- ("r-foreach" ,r-foreach)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsqlite" ,r-rsqlite)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-affyio
+ r-biobase
+ r-biocgenerics
+ r-biocmanager
+ r-biostrings
+ r-dbi
+ r-ff
+ r-foreach
+ r-genomicranges
+ r-iranges
+ r-rsqlite
+ r-s4vectors
+ r-summarizedexperiment))
(home-page "https://bioconductor.org/packages/oligoClasses/")
(synopsis "Classes for high-throughput arrays")
(description
@@ -5077,21 +4981,21 @@ packages.")
"1cmnnq0d5xsjsx8c8n8wcl6l9d31sbglb8yrsibykcvnhw15fsf6"))))
(properties `((upstream-name . "oligo")))
(build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-affxparser" ,r-affxparser)
- ("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-ff" ,r-ff)
- ("r-oligoclasses" ,r-oligoclasses)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-rsqlite" ,r-rsqlite)
- ("r-zlibbioc" ,r-zlibbioc)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (inputs (list zlib))
+ (propagated-inputs
+ (list r-affxparser
+ r-affyio
+ r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-dbi
+ r-ff
+ r-oligoclasses
+ r-preprocesscore
+ r-rsqlite
+ r-zlibbioc))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/oligo/")
(synopsis "Preprocessing tools for oligonucleotide arrays")
(description
@@ -5113,10 +5017,9 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
"1mn2qmqn89lfsx7rg54d1lwz45bfx0b91q6ahf43a1yzrrhwn138"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)
- ("r-reshape2" ,r-reshape2)))
+ (list r-ggplot2 r-reshape2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/StoreyLab/qvalue")
(synopsis "Q-value estimation for false discovery rate control")
(description
@@ -5168,13 +5071,13 @@ integration with @code{Rcpp}.")
(properties `((upstream-name . "apeglm")))
(build-system r-build-system)
(propagated-inputs
- `(("r-emdbook" ,r-emdbook)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppnumerical" ,r-rcppnumerical)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-emdbook
+ r-genomicranges
+ r-rcpp
+ r-rcppeigen
+ r-rcppnumerical
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/apeglm")
(synopsis "Approximate posterior estimation for GLM coefficients")
(description "This package provides Bayesian shrinkage estimators for
@@ -5195,14 +5098,14 @@ posterior for individual coefficients.")
(properties `((upstream-name . "GreyListChIP")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-mass" ,r-mass)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-bsgenome
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-mass
+ r-rsamtools
+ r-rtracklayer
+ r-summarizedexperiment))
(home-page "https://bioconductor.org/packages/GreyListChIP")
(synopsis "Greylist artefact regions based on ChIP inputs")
(description "This package identifies regions of ChIP experiments with high
@@ -5223,29 +5126,29 @@ signal in the input, that lead to spurious peaks during peak calling.")
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
- `(("r-amap" ,r-amap)
- ("r-apeglm" ,r-apeglm)
- ("r-ashr" ,r-ashr)
- ("r-biocparallel" ,r-biocparallel)
- ("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gplots" ,r-gplots)
- ("r-greylistchip" ,r-greylistchip)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)
- ("r-locfit" ,r-locfit)
- ("r-rcolorbrewer" , r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-systempiper" ,r-systempiper)))
+ (list r-amap
+ r-apeglm
+ r-ashr
+ r-biocparallel
+ r-deseq2
+ r-dplyr
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-gplots
+ r-greylistchip
+ r-iranges
+ r-lattice
+ r-limma
+ r-locfit
+ r-rcolorbrewer
+ r-rcpp
+ r-rhtslib
+ r-rsamtools
+ r-s4vectors
+ r-summarizedexperiment
+ r-systempiper))
(home-page "https://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
@@ -5268,13 +5171,13 @@ occupancy (overlap) analysis and plotting functions.")
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
- `(("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-genomicranges" ,r-genomicranges)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-rsamtools" ,r-rsamtools)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-rtracklayer" ,r-rtracklayer)))
+ (list r-s4vectors
+ r-iranges
+ r-genomicranges
+ r-summarizedexperiment
+ r-rsamtools
+ r-genomicalignments
+ r-rtracklayer))
(home-page "https://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
@@ -5299,20 +5202,20 @@ processing to visualization and annotation.")
"03hpj218s8fynmk1s50s0rinhsljikxdrff06yc8ysbyc6hyfb4k"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-benchmarkme" ,r-benchmarkme)
- ("r-biocparallel" ,r-biocparallel)
- ("r-clusterr" ,r-clusterr)
- ("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-knitr))
+ (propagated-inputs
+ (list r-beachmat
+ r-benchmarkme
+ r-biocparallel
+ r-clusterr
+ r-delayedarray
+ r-matrix
+ r-rcpp
+ r-rcpparmadillo
+ r-rhdf5lib
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment))
(home-page "https://bioconductor.org/packages/mbkmeans")
(synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
(description "This package implements the mini-batch k-means algorithm for
@@ -5332,10 +5235,7 @@ large datasets, including support for on-disk data representation.")
"03z71r7g318nwwgiz0k8qwbhghw1hhdhh1an4qnb0nc62c5x9kns"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-survival" ,r-survival)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biobase" ,r-biobase)
- ("r-mass" ,r-mass)))
+ (list r-survival r-biocgenerics r-biobase r-mass))
(home-page "https://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
@@ -5369,7 +5269,7 @@ expressed genes in DNA microarray experiments.")
"0x31lz3qimxmng6w99xnqazaj943d94b04nbziad4jfv7c1bc2h0"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)))
+ (list r-biocgenerics))
(home-page "https://bioconductor.org/packages/graph")
(synopsis "Handle graph data structures in R")
(description
@@ -5391,8 +5291,7 @@ expressed genes in DNA microarray experiments.")
(properties `((upstream-name . "ggm")))
(build-system r-build-system)
(propagated-inputs
- `(("r-graph" ,r-graph)
- ("r-igraph" ,r-igraph)))
+ (list r-graph r-igraph))
(home-page "https://cran.r-project.org/package=ggm")
(synopsis "Functions for graphical Markov models")
(description
@@ -5415,9 +5314,7 @@ fitting of some classes of graphical Markov models.")
(properties `((upstream-name . "PerfMeas")))
(build-system r-build-system)
(propagated-inputs
- `(("r-graph" ,r-graph)
- ("r-limma" ,r-limma)
- ("r-rbgl" ,r-rbgl)))
+ (list r-graph r-limma r-rbgl))
(home-page "https://cran.r-project.org/web/packages/PerfMeas/")
(synopsis "Performance measures for ranking and classification tasks")
(description
@@ -5441,9 +5338,7 @@ a given recall, F-score for single and multiple classes are available.")
(properties `((upstream-name . "CodeDepends")))
(build-system r-build-system)
(propagated-inputs
- `(("r-codetools" ,r-codetools)
- ("r-graph" ,r-graph)
- ("r-xml" ,r-xml)))
+ (list r-codetools r-graph r-xml))
(home-page "https://cran.r-project.org/web/packages/CodeDepends")
(synopsis "Analysis of R code for reproducible research and code comprehension")
(description
@@ -5469,33 +5364,33 @@ determining dependencies between variables, code improvement suggestions.")
(properties `((upstream-name . "ChIPpeakAnno")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-dplyr" ,r-dplyr)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-graph" ,r-graph)
- ("r-interactionset" ,r-interactionset)
- ("r-iranges" ,r-iranges)
- ("r-keggrest" ,r-keggrest)
- ("r-matrixstats" ,r-matrixstats)
- ("r-multtest" ,r-multtest)
- ("r-rbgl" ,r-rbgl)
- ("r-regioner" ,r-regioner)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-venndiagram" ,r-venndiagram)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biocgenerics
+ r-biomart
+ r-biostrings
+ r-dbi
+ r-dplyr
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-graph
+ r-interactionset
+ r-iranges
+ r-keggrest
+ r-matrixstats
+ r-multtest
+ r-rbgl
+ r-regioner
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-summarizedexperiment
+ r-venndiagram))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ChIPpeakAnno")
(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
(description
@@ -5523,7 +5418,7 @@ enrichedGO (addGeneIDs).")
`((upstream-name . "MatrixGenerics")))
(build-system r-build-system)
(propagated-inputs
- `(("r-matrixstats" ,r-matrixstats)))
+ (list r-matrixstats))
(home-page "https://bioconductor.org/packages/MatrixGenerics")
(synopsis "S4 generic summary statistic functions for matrix-like objects")
(description
@@ -5547,7 +5442,7 @@ incompatibilities.")
(base32 "1la805y8j522vpiazm1z6wpq4ibia9bib5fpiia5mxmpzmqg6gzz"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-limma" ,r-limma)))
+ (list r-limma))
(home-page "https://bioconductor.org/packages/marray")
(synopsis "Exploratory analysis for two-color spotted microarray data")
(description "This package contains class definitions for two-color spotted
@@ -5567,8 +5462,7 @@ normalization and quality checking.")
(properties `((upstream-name . "CGHbase")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-marray" ,r-marray)))
+ (list r-biobase r-marray))
(home-page "https://bioconductor.org/packages/CGHbase")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
@@ -5587,11 +5481,7 @@ the @code{arrayCGH} packages.")
(properties `((upstream-name . "CGHcall")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-cghbase" ,r-cghbase)
- ("r-impute" ,r-impute)
- ("r-dnacopy" ,r-dnacopy)
- ("r-snowfall" ,r-snowfall)))
+ (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
(home-page "https://bioconductor.org/packages/CGHcall")
(synopsis "Base functions and classes for arrayCGH data analysis")
(description "This package contains functions and classes that are needed by
@@ -5610,16 +5500,16 @@ the @code{arrayCGH} packages.")
(properties `((upstream-name . "QDNAseq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-cghbase" ,r-cghbase)
- ("r-cghcall" ,r-cghcall)
- ("r-dnacopy" ,r-dnacopy)
- ("r-future-apply" ,r-future-apply)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-r-utils" ,r-r-utils)
- ("r-rsamtools" ,r-rsamtools)))
+ (list r-biobase
+ r-cghbase
+ r-cghcall
+ r-dnacopy
+ r-future-apply
+ r-genomicranges
+ r-iranges
+ r-matrixstats
+ r-r-utils
+ r-rsamtools))
(home-page "https://bioconductor.org/packages/QDNAseq")
(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
(description "The genome is divided into non-overlapping fixed-sized bins,
@@ -5644,9 +5534,7 @@ respectively.")
(properties `((upstream-name . "baySeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-edger" ,r-edger)
- ("r-genomicranges" ,r-genomicranges)))
+ (list r-abind r-edger r-genomicranges))
(home-page "https://bioconductor.org/packages/baySeq/")
(synopsis "Bayesian analysis of differential expression patterns in count data")
(description
@@ -5670,16 +5558,16 @@ more complex hypotheses) via empirical Bayesian methods.")
(properties `((upstream-name . "ChIPComp")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-bsgenome-mmusculus-ucsc-mm9
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-limma
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/ChIPComp")
(synopsis "Quantitative comparison of multiple ChIP-seq datasets")
(description
@@ -5704,24 +5592,24 @@ datasets.")
(properties `((upstream-name . "RiboProfiling")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-data-table" ,r-data-table)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-plyr" ,r-plyr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-sqldf" ,r-sqldf)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-data-table
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggbio
+ r-ggplot2
+ r-iranges
+ r-plyr
+ r-reshape2
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-sqldf))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/RiboProfiling/")
(synopsis "Ribosome profiling data analysis")
(description "Starting with a BAM file, this package provides the
@@ -5745,13 +5633,13 @@ assessment, principal component analysis on codon coverage.")
(properties `((upstream-name . "riboSeqR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-bayseq" ,r-bayseq)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-seqlogo" ,r-seqlogo)))
+ (list r-abind
+ r-bayseq
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-rsamtools
+ r-seqlogo))
(home-page "https://bioconductor.org/packages/riboSeqR/")
(synopsis "Analysis of sequencing data from ribosome profiling experiments")
(description
@@ -5774,16 +5662,16 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
`((upstream-name . "InteractionSet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocgenerics
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rcpp
+ r-s4vectors
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/InteractionSet")
(synopsis "Base classes for storing genomic interaction data")
(description
@@ -5808,24 +5696,24 @@ experiments.")
`((upstream-name . "GenomicInteractions")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-gviz" ,r-gviz)
- ("r-igraph" ,r-igraph)
- ("r-interactionset" ,r-interactionset)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-data-table
+ r-dplyr
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-gridextra
+ r-gviz
+ r-igraph
+ r-interactionset
+ r-iranges
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-stringr))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
(synopsis "R package for handling genomic interaction data")
(description
@@ -5846,7 +5734,7 @@ information and producing various plots and statistics.")
(base32
"1yq5igwzcwfhxy49qf3pralpikiqq7sqr1cig8mkpjpaj5bbaayx"))))
(build-system r-build-system)
- (propagated-inputs `(("r-amap" ,r-amap)))
+ (propagated-inputs (list r-amap))
(home-page "https://bioconductor.org/packages/ctc/")
(synopsis "Cluster and tree conversion")
(description
@@ -5867,12 +5755,12 @@ trees and clusters to other programs.")
"1psl9mqgx1d21kayaxvrxriw34fq30wnd57q5c1sk3p8iahg73g0"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biasedurn" ,r-biasedurn)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genelendatabase" ,r-genelendatabase)
- ("r-go-db" ,r-go-db)
- ("r-mgcv" ,r-mgcv)))
+ (list r-annotationdbi
+ r-biasedurn
+ r-biocgenerics
+ r-genelendatabase
+ r-go-db
+ r-mgcv))
(home-page "https://bioconductor.org/packages/goseq/")
(synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
(description
@@ -5894,15 +5782,15 @@ defined categories which are over/under represented in RNA-seq data.")
(properties `((upstream-name . "Glimma")))
(build-system r-build-system)
(propagated-inputs
- `(("r-deseq2" ,r-deseq2)
- ("r-edger" ,r-edger)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-jsonlite" ,r-jsonlite)
- ("r-limma" ,r-limma)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-deseq2
+ r-edger
+ r-htmlwidgets
+ r-jsonlite
+ r-limma
+ r-s4vectors
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/Shians/Glimma")
(synopsis "Interactive HTML graphics")
(description
@@ -5927,8 +5815,7 @@ information.")
(properties `((upstream-name . "ROTS")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-rcpp" ,r-rcpp)))
+ (list r-biobase r-rcpp))
(home-page "https://bioconductor.org/packages/ROTS/")
(synopsis "Reproducibility-Optimized Test Statistic")
(description
@@ -5950,8 +5837,7 @@ in omics data.")
"06w8xlw4j1fc9ipdgw55dvhp07f04icmhr20lqzwwhqd5pskrra3"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-mass" ,r-mass)))
+ (list r-biobase r-mass))
(home-page "http://www.genopolis.it")
(synopsis "Detect differential expression in microarray and proteomics datasets")
(description
@@ -5976,30 +5862,29 @@ genes or proteins in these datasets.")
(properties `((upstream-name . "INSPEcT")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-deseq2" ,r-deseq2)
- ("r-desolve" ,r-desolve)
- ("r-gdata" ,r-gdata)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-plgem" ,r-plgem)
- ("r-proc" ,r-proc)
- ("r-rootsolve" ,r-rootsolve)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-txdb-mmusculus-ucsc-mm9-knowngene"
- ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-deseq2
+ r-desolve
+ r-gdata
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-kernsmooth
+ r-plgem
+ r-proc
+ r-rootsolve
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-shiny
+ r-summarizedexperiment
+ r-txdb-mmusculus-ucsc-mm9-knowngene))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/INSPEcT")
(synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
(description
@@ -6023,11 +5908,9 @@ modeling the rates that determines changes in mature mRNA levels.")
(properties `((upstream-name . "DNABarcodes")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)))
+ (list r-bh r-matrix r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/DNABarcodes")
(synopsis "Create and analyze DNA barcodes")
(description
@@ -6052,12 +5935,9 @@ demultiplexed, i.e. assigned to their original reference barcode.")
(properties `((upstream-name . "RUVSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-edaseq" ,r-edaseq)
- ("r-edger" ,r-edger)
- ("r-mass" ,r-mass)))
+ (list r-biobase r-edaseq r-edger r-mass))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/drisso/RUVSeq")
(synopsis "Remove unwanted variation from RNA-Seq data")
(description
@@ -6080,13 +5960,9 @@ samples.")
(properties `((upstream-name . "BiocNeighbors")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpphnsw" ,r-rcpphnsw)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocNeighbors")
(synopsis "Nearest Neighbor Detection for Bioconductor packages")
(description
@@ -6112,10 +5988,8 @@ achieved for all methods using the BiocParallel framework.")
(properties `((upstream-name . "ScaledMatrix")))
(build-system r-build-system)
(propagated-inputs
- `(("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-delayedarray r-matrix r-s4vectors))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/LTLA/ScaledMatrix")
(synopsis "Create a DelayedMatrix of scaled and centered values")
(description
@@ -6140,14 +6014,14 @@ multiplication.")
(properties `((upstream-name . "treeio")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-dplyr" ,r-dplyr)
- ("r-jsonlite" ,r-jsonlite)
- ("r-magrittr" ,r-magrittr)
- ("r-rlang" ,r-rlang)
- ("r-tibble" ,r-tibble)
- ("r-tidytree" ,r-tidytree)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-ape
+ r-dplyr
+ r-jsonlite
+ r-magrittr
+ r-rlang
+ r-tibble
+ r-tidytree))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/YuLab-SMU/treeio")
(synopsis "Base classes and functions for Phylogenetic tree input and output")
(description
@@ -6172,20 +6046,20 @@ platform for merging tree with associated data and converting file formats.")
(properties `((upstream-name . "ggtree")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-aplot" ,r-aplot)
- ("r-dplyr" ,r-dplyr)
- ("r-ggfun" ,r-ggfun)
- ("r-ggplot2" ,r-ggplot2)
- ("r-magrittr" ,r-magrittr)
- ("r-purrr" ,r-purrr)
- ("r-rlang" ,r-rlang)
- ("r-scales" ,r-scales)
- ("r-tidyr" ,r-tidyr)
- ("r-tidytree" ,r-tidytree)
- ("r-treeio" ,r-treeio)
- ("r-yulab-utils" ,r-yulab-utils)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-ape
+ r-aplot
+ r-dplyr
+ r-ggfun
+ r-ggplot2
+ r-magrittr
+ r-purrr
+ r-rlang
+ r-scales
+ r-tidyr
+ r-tidytree
+ r-treeio
+ r-yulab-utils))
+ (native-inputs (list r-knitr))
(home-page "https://yulab-smu.top/treedata-book/")
(synopsis "R package for visualization of trees and annotation data")
(description
@@ -6209,9 +6083,9 @@ data.")
(properties `((upstream-name . "metapod")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcpp" ,r-rcpp)))
+ (list r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/metapod")
(synopsis "Meta-analyses on p-values of differential analyses")
(description
@@ -6238,18 +6112,18 @@ missing values and weighting where appropriate.")
(properties `((upstream-name . "BiocSingular")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-delayedarray" ,r-delayedarray)
- ("r-irlba" ,r-irlba)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rsvd" ,r-rsvd)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scaledmatrix" ,r-scaledmatrix)))
+ (list r-beachmat
+ r-biocgenerics
+ r-biocparallel
+ r-delayedarray
+ r-irlba
+ r-matrix
+ r-rcpp
+ r-rsvd
+ r-s4vectors
+ r-scaledmatrix))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/LTLA/BiocSingular")
(synopsis "Singular value decomposition for Bioconductor packages")
(description
@@ -6272,30 +6146,30 @@ possible, parallelization is achieved using the BiocParallel framework.")
"1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-ggplot-multistats" ,r-ggplot-multistats)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggthemes" ,r-ggthemes)
- ("r-irlba" ,r-irlba)
- ("r-knn-covertree" ,r-knn-covertree)
- ("r-matrix" ,r-matrix)
- ("r-pcamethods" ,r-pcamethods)
- ("r-proxy" ,r-proxy)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcpphnsw" ,r-rcpphnsw)
- ("r-rspectra" ,r-rspectra)
- ("r-scales" ,r-scales)
- ("r-scatterplot3d" ,r-scatterplot3d)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-smoother" ,r-smoother)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tidyr" ,r-tidyr)
- ("r-tidyselect" ,r-tidyselect)
- ("r-vim" ,r-vim)))
- (native-inputs
- `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
+ (list r-biobase
+ r-biocgenerics
+ r-ggplot-multistats
+ r-ggplot2
+ r-ggthemes
+ r-irlba
+ r-knn-covertree
+ r-matrix
+ r-pcamethods
+ r-proxy
+ r-rcpp
+ r-rcppeigen
+ r-rcpphnsw
+ r-rspectra
+ r-scales
+ r-scatterplot3d
+ r-singlecellexperiment
+ r-smoother
+ r-summarizedexperiment
+ r-tidyr
+ r-tidyselect
+ r-vim))
+ (native-inputs
+ (list r-nbconvertr)) ; for vignettes
(home-page "https://bioconductor.org/packages/destiny/")
(synopsis "Create and plot diffusion maps")
(description "This package provides tools to create and plot diffusion
@@ -6317,11 +6191,7 @@ maps.")
(properties `((upstream-name . "savR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-reshape2" ,r-reshape2)
- ("r-scales" ,r-scales)
- ("r-xml" ,r-xml)))
+ (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
(home-page "https://github.com/bcalder/savR")
(synopsis "Parse and analyze Illumina SAV files")
(description
@@ -6343,25 +6213,25 @@ Viewer (SAV) files, access data, and generate QC plots.")
(properties `((upstream-name . "ChIPexoQual")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-biovizbase" ,r-biovizbase)
- ("r-broom" ,r-broom)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hexbin" ,r-hexbin)
- ("r-iranges" ,r-iranges)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocparallel
+ r-biovizbase
+ r-broom
+ r-data-table
+ r-dplyr
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-hexbin
+ r-iranges
+ r-rcolorbrewer
+ r-rmarkdown
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-viridis))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/keleslab/ChIPexoQual")
(synopsis "Quality control pipeline for ChIP-exo/nexus data")
(description
@@ -6381,10 +6251,7 @@ sequencing data.")
"143ifvjkjz0392drm82xmpj1f8b5pc2dyyxyc9dkqmay8lf1n534"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-genomicranges" ,r-genomicranges)
- ("r-biocgenerics" ,r-biocgenerics)))
+ (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
(home-page "https://bioconductor.org/packages/copynumber")
(synopsis "Segmentation of single- and multi-track copy number data")
(description
@@ -6405,7 +6272,7 @@ penalized least squares regression method.")
"19ax431i97r49gh1232vf8mgmkvc6k26lnq44j3g10n6q01czswm"))))
(properties `((upstream-name . "DNAcopy")))
(build-system r-build-system)
- (native-inputs `(("gfortran" ,gfortran)))
+ (native-inputs (list gfortran))
(home-page "https://bioconductor.org/packages/DNAcopy")
(synopsis "DNA copy number data analysis")
(description
@@ -6430,9 +6297,7 @@ abnormal copy number.")
(properties `((upstream-name . "HTSCluster")))
(build-system r-build-system)
(propagated-inputs
- `(("r-capushe" ,r-capushe)
- ("r-edger" ,r-edger)
- ("r-plotrix" ,r-plotrix)))
+ (list r-capushe r-edger r-plotrix))
(home-page "https://cran.r-project.org/web/packages/HTSCluster")
(synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
(description
@@ -6484,7 +6349,7 @@ and summarizing a set of statistics using a weighted distance approach.")
(properties `((upstream-name . "NBPSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-qvalue" ,r-qvalue)))
+ (list r-qvalue))
(home-page "https://cran.r-project.org/web/packages/NBPSeq")
(synopsis "Negative binomial models for RNA-Seq data")
(description
@@ -6506,9 +6371,7 @@ and regression inferences from RNA-sequencing data.")
(properties `((upstream-name . "EBSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-blockmodeling" ,r-blockmodeling)
- ("r-gplots" ,r-gplots)
- ("r-testthat" ,r-testthat)))
+ (list r-blockmodeling r-gplots r-testthat))
(home-page "https://bioconductor.org/packages/EBSeq")
(synopsis "Differential expression analysis of RNA-seq data")
(description
@@ -6528,23 +6391,23 @@ gene and isoform level using RNA-seq data")
"0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-bamsignals" ,r-bamsignals)
- ("r-bezier" ,r-bezier)
- ("r-biovizbase" ,r-biovizbase)
- ("r-digest" ,r-digest)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-memoise" ,r-memoise)
- ("r-regioner" ,r-regioner)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-bamsignals
+ r-bezier
+ r-biovizbase
+ r-digest
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-memoise
+ r-regioner
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/karyoploteR/")
(synopsis "Plot customizable linear genomes displaying arbitrary data")
(description "This package creates karyotype plots of arbitrary genomes and
@@ -6567,10 +6430,9 @@ coordinates.")
"1bv28b1fgcazv6j0xw4nn6wljs37qnkyahqy7anrwissdpryhjfs"))))
(build-system r-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
+ (list pkg-config r-knitr))
(home-page "https://r-forge.r-project.org/projects/rsymphony")
(synopsis "Symphony integer linear programming solver in R")
(description
@@ -6598,12 +6460,9 @@ to install interface to SYMPHONY.")
(properties `((upstream-name . "IHW")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-fdrtool" ,r-fdrtool)
- ("r-lpsymphony" ,r-lpsymphony)
- ("r-slam" ,r-slam)))
+ (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/IHW")
(synopsis "Independent hypothesis weighting")
(description
@@ -6630,19 +6489,19 @@ independent of the p-value under the null hypothesis.")
(properties `((upstream-name . "iCOBRA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-ggplot2" ,r-ggplot2)
- ("r-limma" ,r-limma)
- ("r-reshape2" ,r-reshape2)
- ("r-rocr" ,r-rocr)
- ("r-scales" ,r-scales)
- ("r-shiny" ,r-shiny)
- ("r-shinybs" ,r-shinybs)
- ("r-shinydashboard" ,r-shinydashboard)
- ("r-upsetr" ,r-upsetr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-dplyr
+ r-dt
+ r-ggplot2
+ r-limma
+ r-reshape2
+ r-rocr
+ r-scales
+ r-shiny
+ r-shinybs
+ r-shinydashboard
+ r-upsetr))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/iCOBRA")
(synopsis "Comparison and visualization of ranking and assignment methods")
(description
@@ -6667,11 +6526,9 @@ interactive exploration of results.")
`((upstream-name . "ResidualMatrix")))
(build-system r-build-system)
(propagated-inputs
- `(("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-delayedarray r-matrix r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/LTLA/ResidualMatrix")
(synopsis "Create a DelayedMatrix of regression residuals")
(description
@@ -6697,23 +6554,23 @@ multiplication and calculation of row/column sums or means.")
(properties `((upstream-name . "batchelor")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-igraph" ,r-igraph)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-residualmatrix" ,r-residualmatrix)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scaledmatrix" ,r-scaledmatrix)
- ("r-scuttle" ,r-scuttle)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-biocgenerics
+ r-biocneighbors
+ r-biocparallel
+ r-biocsingular
+ r-delayedarray
+ r-delayedmatrixstats
+ r-igraph
+ r-matrix
+ r-rcpp
+ r-residualmatrix
+ r-s4vectors
+ r-scaledmatrix
+ r-scuttle
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/batchelor")
(synopsis "Single-Cell Batch Correction Methods")
(description
@@ -6740,20 +6597,20 @@ the numbers of cells across batches.")
(properties `((upstream-name . "MAST")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-ggplot2" ,r-ggplot2)
- ("r-plyr" ,r-plyr)
- ("r-progress" ,r-progress)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-abind
+ r-biobase
+ r-biocgenerics
+ r-data-table
+ r-ggplot2
+ r-plyr
+ r-progress
+ r-reshape2
+ r-s4vectors
+ r-singlecellexperiment
+ r-stringr
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/RGLab/MAST/")
(synopsis "Model-based analysis of single cell transcriptomics")
(description
@@ -6774,38 +6631,38 @@ single cell assay data.")
"0wb2c1jf502lrfx3d0amb09fvhalrwxvpsp99jsab162v4hddg85"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocviews" ,r-biocviews)
- ("r-cluster" ,r-cluster)
- ("r-combinat" ,r-combinat)
- ("r-ddrtree" ,r-ddrtree)
- ("r-densityclust" ,r-densityclust)
- ("r-dplyr" ,r-dplyr)
- ("r-fastica" ,r-fastica)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hsmmsinglecell" ,r-hsmmsinglecell)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-limma" ,r-limma)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plyr" ,r-plyr)
- ("r-proxy" ,r-proxy)
- ("r-qlcmatrix" ,r-qlcmatrix)
- ("r-rann" ,r-rann)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-rtsne" ,r-rtsne)
- ("r-slam" ,r-slam)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-vgam" ,r-vgam)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocviews
+ r-cluster
+ r-combinat
+ r-ddrtree
+ r-densityclust
+ r-dplyr
+ r-fastica
+ r-ggplot2
+ r-hsmmsinglecell
+ r-igraph
+ r-irlba
+ r-limma
+ r-mass
+ r-matrix
+ r-matrixstats
+ r-pheatmap
+ r-plyr
+ r-proxy
+ r-qlcmatrix
+ r-rann
+ r-rcpp
+ r-reshape2
+ r-rtsne
+ r-slam
+ r-stringr
+ r-tibble
+ r-vgam
+ r-viridis))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/monocle")
(synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
(description
@@ -6837,11 +6694,11 @@ qPCR data, but could be used with other types as well.")
(properties `((upstream-name . "leidenbase")))
(build-system r-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(propagated-inputs
- `(("r-igraph" ,r-igraph)))
+ (list r-igraph))
(home-page "https://github.com/cole-trapnell-lab/leidenbase")
(synopsis "R and C wrappers to run the Leiden find_partition function")
(description
@@ -6870,11 +6727,7 @@ several functions from the R igraph package.")
"13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-generics" ,r-generics)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)))
+ (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
(home-page "https://pneuvial.github.io/sanssouci")
(synopsis "Post Hoc multiple testing inference")
(description
@@ -6899,50 +6752,50 @@ user-defined and/or data-driven sets of hypotheses.")
"16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-batchelor" ,r-batchelor)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dplyr" ,r-dplyr)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-grr" ,r-grr)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-leidenbase" ,r-leidenbase)
- ("r-limma" ,r-limma)
- ("r-lmtest" ,r-lmtest)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-matrix-utils" ,r-matrix-utils)
- ("r-pbapply" ,r-pbapply)
- ("r-pbmcapply" ,r-pbmcapply)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plotly" ,r-plotly)
- ("r-pryr" ,r-pryr)
- ("r-proxy" ,r-proxy)
- ("r-pscl" ,r-pscl)
- ("r-purrr" ,r-purrr)
- ("r-rann" ,r-rann)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppparallel" ,r-rcppparallel)
- ("r-reshape2" ,r-reshape2)
- ("r-reticulate" ,r-reticulate)
- ("r-rhpcblasctl" ,r-rhpcblasctl)
- ("r-rsample" ,r-rsample)
- ("r-rtsne" ,r-rtsne)
- ("r-shiny" ,r-shiny)
- ("r-slam" ,r-slam)
- ("r-spdep" ,r-spdep)
- ("r-speedglm" ,r-speedglm)
- ("r-stringr" ,r-stringr)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-uwot" ,r-uwot)
- ("r-viridis" ,r-viridis)))
+ (list r-assertthat
+ r-batchelor
+ r-biobase
+ r-biocgenerics
+ r-delayedmatrixstats
+ r-dplyr
+ r-ggplot2
+ r-ggrepel
+ r-grr
+ r-htmlwidgets
+ r-igraph
+ r-irlba
+ r-leidenbase
+ r-limma
+ r-lmtest
+ r-mass
+ r-matrix
+ r-matrix-utils
+ r-pbapply
+ r-pbmcapply
+ r-pheatmap
+ r-plotly
+ r-pryr
+ r-proxy
+ r-pscl
+ r-purrr
+ r-rann
+ r-rcpp
+ r-rcppparallel
+ r-reshape2
+ r-reticulate
+ r-rhpcblasctl
+ r-rsample
+ r-rtsne
+ r-shiny
+ r-slam
+ r-spdep
+ r-speedglm
+ r-stringr
+ r-singlecellexperiment
+ r-tibble
+ r-tidyr
+ r-uwot
+ r-viridis))
(home-page "https://github.com/cole-trapnell-lab/monocle3")
(synopsis "Analysis toolkit for single-cell RNA-Seq data")
(description
@@ -6963,8 +6816,7 @@ user-defined and/or data-driven sets of hypotheses.")
(properties `((upstream-name . "NOISeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-matrix" ,r-matrix)))
+ (list r-biobase r-matrix))
(home-page "https://bioconductor.org/packages/NOISeq")
(synopsis "Exploratory analysis and differential expression for RNA-seq data")
(description
@@ -6990,19 +6842,19 @@ assumptions.")
(properties `((upstream-name . "scDD")))
(build-system r-build-system)
(propagated-inputs
- `(("r-arm" ,r-arm)
- ("r-biocparallel" ,r-biocparallel)
- ("r-ebseq" ,r-ebseq)
- ("r-fields" ,r-fields)
- ("r-ggplot2" ,r-ggplot2)
- ("r-mclust" ,r-mclust)
- ("r-outliers" ,r-outliers)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scran" ,r-scran)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-arm
+ r-biocparallel
+ r-ebseq
+ r-fields
+ r-ggplot2
+ r-mclust
+ r-outliers
+ r-s4vectors
+ r-scran
+ r-singlecellexperiment
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/kdkorthauer/scDD")
(synopsis "Mixture modeling of single-cell RNA-seq data")
(description
@@ -7027,29 +6879,29 @@ distributions.")
"1fqlwg195rzpwh35cj941vhmj2plzpn253skig6glr0z2sirr9r1"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-aroma-light" ,r-aroma-light)
- ("r-biocparallel" ,r-biocparallel)
- ("r-boot" ,r-boot)
- ("r-class" ,r-class)
- ("r-cluster" ,r-cluster)
- ("r-compositions" ,r-compositions)
- ("r-diptest" ,r-diptest)
- ("r-edger" ,r-edger)
- ("r-fpc" ,r-fpc)
- ("r-gplots" ,r-gplots)
- ("r-hexbin" ,r-hexbin)
- ("r-limma" ,r-limma)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-matrixstats" ,r-matrixstats)
- ("r-mixtools" ,r-mixtools)
- ("r-rarpack" ,r-rarpack)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rhdf5" ,r-rhdf5)
- ("r-ruvseq" ,r-ruvseq)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-aroma-light
+ r-biocparallel
+ r-boot
+ r-class
+ r-cluster
+ r-compositions
+ r-diptest
+ r-edger
+ r-fpc
+ r-gplots
+ r-hexbin
+ r-limma
+ r-matrixgenerics
+ r-matrixstats
+ r-mixtools
+ r-rarpack
+ r-rcolorbrewer
+ r-rhdf5
+ r-ruvseq
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/scone")
(synopsis "Single cell overview of normalized expression data")
(description
@@ -7072,18 +6924,18 @@ high-throughput analyses.")
(properties `((upstream-name . "GEOquery")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-limma" ,r-limma)
- ("r-magrittr" ,r-magrittr)
- ("r-r-utils" ,r-r-utils)
- ("r-readr" ,r-readr)
- ("r-tidyr" ,r-tidyr)
- ("r-xml2" ,r-xml2)))
+ (list r-biobase
+ r-data-table
+ r-dplyr
+ r-httr
+ r-limma
+ r-magrittr
+ r-r-utils
+ r-readr
+ r-tidyr
+ r-xml2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/seandavi/GEOquery/")
(synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
(description
@@ -7106,7 +6958,7 @@ the bridge between GEO and BioConductor.")
"0icsp610am5vrd8x2h9c450phn4vl9c5wnzqmkix5hkqzrykk34m"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-base64" ,r-base64)))
+ (list r-base64))
(home-page "https://github.com/HenrikBengtsson/illuminaio/")
(synopsis "Parse Illumina microarray output files")
(description
@@ -7127,9 +6979,7 @@ files, including IDAT.")
"1fymp5ci1nwkk5yfj7hli464xqvvlvzf2a5j0w3qkxly9hrymix9"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-multtest" ,r-multtest)
- ("r-scrime" ,r-scrime)))
+ (list r-biobase r-multtest r-scrime))
(home-page "https://bioconductor.org/packages/siggenes/")
(synopsis
"Multiple testing using SAM and Efron's empirical Bayes approaches")
@@ -7153,19 +7003,19 @@ Bayes Analyses of Microarrays} (EBAM).")
"0d5cz9xy7vhcaj5n3h4cfiv08sn7wn83458525pdwvdzzm449xgv"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dorng" ,r-dorng)
- ("r-foreach" ,r-foreach)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-iterators" ,r-iterators)
- ("r-limma" ,r-limma)
- ("r-locfit" ,r-locfit)
- ("r-matrixstats" ,r-matrixstats)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-annotationdbi
+ r-biocgenerics
+ r-dorng
+ r-foreach
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-iterators
+ r-limma
+ r-locfit
+ r-matrixstats
+ r-s4vectors))
(home-page "https://github.com/ririzarr/bumphunter")
(synopsis "Find bumps in genomic data")
(description
@@ -7187,37 +7037,37 @@ studies.")
"0d5220nknwgi1020vhvf7408n5p80dmad66n85af5776qn84a6nx"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-beanplot" ,r-beanplot)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bumphunter" ,r-bumphunter)
- ("r-data-table" ,r-data-table)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-genefilter" ,r-genefilter)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-geoquery" ,r-geoquery)
- ("r-hdf5array" ,r-hdf5array)
- ("r-illuminaio" ,r-illuminaio)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-limma" ,r-limma)
- ("r-mass" ,r-mass)
- ("r-mclust" ,r-mclust)
- ("r-nlme" ,r-nlme)
- ("r-nor1mix" ,r-nor1mix)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-quadprog" ,r-quadprog)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape" ,r-reshape)
- ("r-s4vectors" ,r-s4vectors)
- ("r-siggenes" ,r-siggenes)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-beanplot
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bumphunter
+ r-data-table
+ r-delayedarray
+ r-delayedmatrixstats
+ r-genefilter
+ r-genomeinfodb
+ r-genomicranges
+ r-geoquery
+ r-hdf5array
+ r-illuminaio
+ r-iranges
+ r-lattice
+ r-limma
+ r-mass
+ r-mclust
+ r-nlme
+ r-nor1mix
+ r-preprocesscore
+ r-quadprog
+ r-rcolorbrewer
+ r-reshape
+ r-s4vectors
+ r-siggenes
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/hansenlab/minfi")
(synopsis "Analyze Illumina Infinium DNA methylation arrays")
(description
@@ -7238,27 +7088,27 @@ methylation arrays.")
"1lfcsv8k9c4ndfwlbdk3vd7fq58100bfijyxklna41zf8m8kkkka"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
- ("r-genefilter" ,r-genefilter)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-illuminaio" ,r-illuminaio)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-matrixstats" ,r-matrixstats)
- ("r-minfi" ,r-minfi)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotate
+ r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-fdb-infiniummethylation-hg19
+ r-genefilter
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-illuminaio
+ r-iranges
+ r-lattice
+ r-matrixstats
+ r-minfi
+ r-reshape2
+ r-s4vectors
+ r-scales
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/methylumi")
(synopsis "Handle Illumina methylation data")
(description
@@ -7285,21 +7135,21 @@ and Infinium HD arrays are also included.")
"0v33p66vn4alhx2il9wwdvc9sqvgasgj0s2gk85gjc76ad0017in"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-annotate" ,r-annotate)
- ("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-dbi" ,r-dbi)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-methylumi" ,r-methylumi)
- ("r-mgcv" ,r-mgcv)
- ("r-nleqslv" ,r-nleqslv)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-rsqlite" ,r-rsqlite)))
+ (list r-affy
+ r-annotate
+ r-annotationdbi
+ r-biobase
+ r-dbi
+ r-genomicfeatures
+ r-genomicranges
+ r-kernsmooth
+ r-lattice
+ r-mass
+ r-methylumi
+ r-mgcv
+ r-nleqslv
+ r-preprocesscore
+ r-rsqlite))
(home-page "https://bioconductor.org/packages/lumi")
(synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
(description
@@ -7325,26 +7175,26 @@ especially Illumina Infinium methylation microarrays.")
(properties `((upstream-name . "Linnorm")))
(build-system r-build-system)
(propagated-inputs
- `(("r-amap" ,r-amap)
- ("r-apcluster" ,r-apcluster)
- ("r-ellipse" ,r-ellipse)
- ("r-fastcluster" ,r-fastcluster)
- ("r-fpc" ,r-fpc)
- ("r-ggdendro" ,r-ggdendro)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gmodels" ,r-gmodels)
- ("r-igraph" ,r-igraph)
- ("r-limma" ,r-limma)
- ("r-mass" ,r-mass)
- ("r-mclust" ,r-mclust)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rtsne" ,r-rtsne)
- ("r-statmod" ,r-statmod)
- ("r-vegan" ,r-vegan)
- ("r-zoo" ,r-zoo)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-amap
+ r-apcluster
+ r-ellipse
+ r-fastcluster
+ r-fpc
+ r-ggdendro
+ r-ggplot2
+ r-gmodels
+ r-igraph
+ r-limma
+ r-mass
+ r-mclust
+ r-rcpp
+ r-rcpparmadillo
+ r-rtsne
+ r-statmod
+ r-vegan
+ r-zoo))
+ (native-inputs
+ (list r-knitr))
(home-page "http://www.jjwanglab.org/Linnorm/")
(synopsis "Linear model and normality based transformation method")
(description
@@ -7386,21 +7236,21 @@ evaluation of DEG analysis methods.")
(properties `((upstream-name . "IONiseR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bit64" ,r-bit64)
- ("r-dplyr" ,r-dplyr)
- ("r-ggplot2" ,r-ggplot2)
- ("r-magrittr" ,r-magrittr)
- ("r-rhdf5" ,r-rhdf5)
- ("r-shortread" ,r-shortread)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bit64
+ r-dplyr
+ r-ggplot2
+ r-magrittr
+ r-rhdf5
+ r-shortread
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-xvector))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/IONiseR/")
(synopsis "Quality assessment tools for Oxford Nanopore MinION data")
(description
@@ -7427,10 +7277,7 @@ surface of a flowcell.")
(properties `((upstream-name . "mutoss")))
(build-system r-build-system)
(propagated-inputs
- `(("r-multcomp" ,r-multcomp)
- ("r-multtest" ,r-multtest)
- ("r-mvtnorm" ,r-mvtnorm)
- ("r-plotrix" ,r-plotrix)))
+ (list r-multcomp r-multtest r-mvtnorm r-plotrix))
(home-page "https://github.com/kornl/mutoss/")
(synopsis "Unified multiple testing procedures")
(description
@@ -7455,10 +7302,7 @@ are standardized and usable by the accompanying mutossGUI package.")
"1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-lattice" ,r-lattice)
- ("r-mutoss" ,r-mutoss)
- ("r-rdpack" ,r-rdpack)
- ("r-tfisher" ,r-tfisher)))
+ (list r-lattice r-mutoss r-rdpack r-tfisher))
(home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
(synopsis "Meta-analysis of significance values")
(description
@@ -7481,28 +7325,28 @@ published results; and a routine for graphical display.")
"1s5anbb38gi5sfkxy19zpvkj8d0ij7m6cd0z4gmx4f5pf7pz0m3j"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocparallel" ,r-biocparallel)
- ("r-edger" ,r-edger)
- ("r-ggplot2" ,r-ggplot2)
- ("r-igraph" ,r-igraph)
- ("r-magrittr" ,r-magrittr)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-mgcv" ,r-mgcv)
- ("r-pbapply" ,r-pbapply)
- ("r-princurve" ,r-princurve)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-slingshot" ,r-slingshot)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tibble" ,r-tibble)
- ("r-trajectoryutils" ,r-trajectoryutils)
- ("r-viridis" ,r-viridis)))
+ (list r-biobase
+ r-biocparallel
+ r-edger
+ r-ggplot2
+ r-igraph
+ r-magrittr
+ r-mass
+ r-matrix
+ r-matrixstats
+ r-mgcv
+ r-pbapply
+ r-princurve
+ r-rcolorbrewer
+ r-s4vectors
+ r-singlecellexperiment
+ r-slingshot
+ r-summarizedexperiment
+ r-tibble
+ r-trajectoryutils
+ r-viridis))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://statomics.github.io/tradeSeq/index.html")
(synopsis "Trajectory-based differential expression analysis")
(description
@@ -7529,9 +7373,7 @@ performs inference on the parameters of the GAM.")
"089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-iranges" ,r-iranges)
- ("r-yaml" ,r-yaml)))
+ (list r-biocgenerics r-iranges r-yaml))
(home-page "https://bioconductor.org/packages/triform/")
(synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
(description
@@ -7554,20 +7396,20 @@ peak definition in combination with known profile characteristics.")
(properties `((upstream-name . "VariantTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-variantannotation" ,r-variantannotation)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-variantannotation))
(home-page "https://bioconductor.org/packages/VariantTools/")
(synopsis "Tools for exploratory analysis of variant calls")
(description
@@ -7594,7 +7436,7 @@ gmapR.")
(properties `((upstream-name . "Heatplus")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-rcolorbrewer))
(home-page "https://github.com/alexploner/Heatplus")
(synopsis "Heatmaps with row and/or column covariates and colored clusters")
(description
@@ -7619,11 +7461,9 @@ information about samples and features can be added to the plot.")
(properties `((upstream-name . "GOSemSim")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-go-db" ,r-go-db)
- ("r-rcpp" ,r-rcpp)))
+ (list r-annotationdbi r-go-db r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://guangchuangyu.github.io/software/GOSemSim")
(synopsis "GO-terms semantic similarity measures")
(description
@@ -7647,8 +7487,7 @@ sets of GO terms, gene products and gene clusters.")
"0agvcpb3lr9v55h53ywf662gpxayivxacv8dcm526cc8i8hdqa9f"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-multtest" ,r-multtest)
- ("r-qvalue" ,r-qvalue)))
+ (list r-multtest r-qvalue))
(home-page "https://bioconductor.org/packages/anota/")
(synopsis "Analysis of translational activity")
(description
@@ -7700,15 +7539,15 @@ phenotype of interest.")
(properties `((upstream-name . "fcScan")))
(build-system r-build-system)
(propagated-inputs
- `(("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-plyr" ,r-plyr)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-doparallel
+ r-foreach
+ r-genomicranges
+ r-iranges
+ r-plyr
+ r-rtracklayer
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/fcScan")
(synopsis "Detect clusters of coordinates with user defined options")
(description
@@ -7733,16 +7572,16 @@ presence of additional sites within the allowed window size.")
"10flcdm4b1kxnsvhl4k6mwkzb1vbai33k291j8nsrhj2cl5l8gm9"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-biocparallel" ,r-biocparallel)
- ("r-data-table" ,r-data-table)
- ("r-fastmatch" ,r-fastmatch)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)))
+ (list r-bh
+ r-biocparallel
+ r-data-table
+ r-fastmatch
+ r-ggplot2
+ r-gridextra
+ r-matrix
+ r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/ctlab/fgsea/")
(synopsis "Fast gene set enrichment analysis")
(description
@@ -7766,16 +7605,16 @@ to multiple hypothesis correction.")
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocparallel" ,r-biocparallel)
- ("r-do-db" ,r-do-db)
- ("r-fgsea" ,r-fgsea)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gosemsim" ,r-gosemsim)
- ("r-qvalue" ,r-qvalue)
- ("r-reshape2" ,r-reshape2)))
+ (list r-annotationdbi
+ r-biocparallel
+ r-do-db
+ r-fgsea
+ r-ggplot2
+ r-gosemsim
+ r-qvalue
+ r-reshape2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://guangchuangyu.github.io/software/DOSE/")
(synopsis "Disease ontology semantic and enrichment analysis")
(description
@@ -7800,23 +7639,23 @@ data.")
"0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-aplot" ,r-aplot)
- ("r-dose" ,r-dose)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggraph" ,r-ggraph)
- ("r-ggtree" ,r-ggtree)
- ("r-gosemsim" ,r-gosemsim)
- ("r-igraph" ,r-igraph)
- ("r-magrittr" ,r-magrittr)
- ("r-plyr" ,r-plyr)
- ("r-purrr" ,r-purrr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape2" ,r-reshape2)
- ("r-scatterpie" ,r-scatterpie)
- ("r-shadowtext" ,r-shadowtext)
- ("r-yulab-utils" ,r-yulab-utils)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-aplot
+ r-dose
+ r-ggplot2
+ r-ggraph
+ r-ggtree
+ r-gosemsim
+ r-igraph
+ r-magrittr
+ r-plyr
+ r-purrr
+ r-rcolorbrewer
+ r-reshape2
+ r-scatterpie
+ r-shadowtext
+ r-yulab-utils))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/GuangchuangYu/enrichplot")
(synopsis "Visualization of functional enrichment result")
(description
@@ -7840,21 +7679,21 @@ All the visualization methods are developed based on ggplot2 graphics.")
`((upstream-name . "clusterProfiler")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dose" ,r-dose)
- ("r-downloader" ,r-downloader)
- ("r-dplyr" ,r-dplyr)
- ("r-enrichplot" ,r-enrichplot)
- ("r-go-db" ,r-go-db)
- ("r-gosemsim" ,r-gosemsim)
- ("r-magrittr" ,r-magrittr)
- ("r-plyr" ,r-plyr)
- ("r-qvalue" ,r-qvalue)
- ("r-rlang" ,r-rlang)
- ("r-tidyr" ,r-tidyr)
- ("r-yulab-utils" ,r-yulab-utils)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-dose
+ r-downloader
+ r-dplyr
+ r-enrichplot
+ r-go-db
+ r-gosemsim
+ r-magrittr
+ r-plyr
+ r-qvalue
+ r-rlang
+ r-tidyr
+ r-yulab-utils))
+ (native-inputs
+ (list r-knitr))
(home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
(synopsis "Analysis and visualization of functional profiles for gene clusters")
(description
@@ -7874,33 +7713,33 @@ profiles (GO and KEGG) of gene and gene clusters.")
"0riray1f841d5fx6mbcki5xmqz21kg5q5l0qz4pkgg9c1d9f7mbc"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocsingular" ,r-biocsingular)
- ("r-cluster" ,r-cluster)
- ("r-delayedarray" ,r-delayedarray)
- ("r-edger" ,r-edger)
- ("r-hdf5array" ,r-hdf5array)
- ("r-howmany" ,r-howmany)
- ("r-kernlab" ,r-kernlab)
- ("r-limma" ,r-limma)
- ("r-locfdr" ,r-locfdr)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-mbkmeans" ,r-mbkmeans)
- ("r-nmf" ,r-nmf)
- ("r-phylobase" ,r-phylobase)
- ("r-pracma" ,r-pracma)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-zinbwave" ,r-zinbwave)))
+ (list r-knitr))
+ (propagated-inputs
+ (list r-ape
+ r-biocgenerics
+ r-biocsingular
+ r-cluster
+ r-delayedarray
+ r-edger
+ r-hdf5array
+ r-howmany
+ r-kernlab
+ r-limma
+ r-locfdr
+ r-matrix
+ r-matrixstats
+ r-mbkmeans
+ r-nmf
+ r-phylobase
+ r-pracma
+ r-rcolorbrewer
+ r-rcpp
+ r-s4vectors
+ r-scales
+ r-singlecellexperiment
+ r-stringr
+ r-summarizedexperiment
+ r-zinbwave))
(home-page "https://bioconductor.org/packages/clusterExperiment/")
(synopsis "Compare clusterings for single-cell sequencing")
(description "This package provides functionality for running and comparing
@@ -7922,26 +7761,26 @@ expression data sets.")
(properties `((upstream-name . "MLInterfaces")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-cluster" ,r-cluster)
- ("r-fpc" ,r-fpc)
- ("r-gbm" ,r-gbm)
- ("r-gdata" ,r-gdata)
- ("r-genefilter" ,r-genefilter)
- ("r-ggvis" ,r-ggvis)
- ("r-hwriter" ,r-hwriter)
- ("r-magrittr" ,r-magrittr)
- ("r-mass" ,r-mass)
- ("r-mlbench" ,r-mlbench)
- ("r-pls" ,r-pls)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rpart" ,r-rpart)
- ("r-sfsmisc" ,r-sfsmisc)
- ("r-shiny" ,r-shiny)
- ("r-threejs" ,r-threejs)))
+ (list r-annotate
+ r-biobase
+ r-biocgenerics
+ r-cluster
+ r-fpc
+ r-gbm
+ r-gdata
+ r-genefilter
+ r-ggvis
+ r-hwriter
+ r-magrittr
+ r-mass
+ r-mlbench
+ r-pls
+ r-rcolorbrewer
+ r-rcpp
+ r-rpart
+ r-sfsmisc
+ r-shiny
+ r-threejs))
(home-page "https://bioconductor.org/packages/MLInterfaces/")
(synopsis "Interfaces to R machine learning procedures")
(description
@@ -7970,11 +7809,7 @@ data in R and Bioconductor containers.")
(substitute* "DESCRIPTION"
((", KEGG.db") "")))))))
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-dbi" ,r-dbi)
- ("r-go-db" ,r-go-db)))
+ (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
(home-page "https://bioconductor.org/packages/annaffy/")
(synopsis "Annotation tools for Affymetrix biological metadata")
(description
@@ -8000,10 +7835,9 @@ It allows searching of biological metadata using various criteria.")
(properties `((upstream-name . "a4Core")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-glmnet" ,r-glmnet)))
+ (list r-biobase r-glmnet))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/a4Core")
(synopsis "Automated Affymetrix array analysis core package")
(description
@@ -8025,15 +7859,15 @@ arrays.")
(properties `((upstream-name . "a4Classif")))
(build-system r-build-system)
(propagated-inputs
- `(("r-a4core" ,r-a4core)
- ("r-a4preproc" ,r-a4preproc)
- ("r-biobase" ,r-biobase)
- ("r-glmnet" ,r-glmnet)
- ("r-pamr" ,r-pamr)
- ("r-rocr" ,r-rocr)
- ("r-varselrf" ,r-varselrf)))
+ (list r-a4core
+ r-a4preproc
+ r-biobase
+ r-glmnet
+ r-pamr
+ r-rocr
+ r-varselrf))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/a4Classif/")
(synopsis "Automated Affymetrix array analysis classification package")
(description
@@ -8055,10 +7889,9 @@ Affymetrix arrays.")
(properties `((upstream-name . "a4Preproc")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)))
+ (list r-biobase r-biocgenerics))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/a4Preproc/")
(synopsis "Automated Affymetrix array analysis preprocessing package")
(description
@@ -8080,9 +7913,9 @@ is used for preprocessing the arrays.")
(properties `((upstream-name . "a4Reporting")))
(build-system r-build-system)
(propagated-inputs
- `(("r-xtable" ,r-xtable)))
+ (list r-xtable))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/a4Reporting/")
(synopsis "Automated Affymetrix array analysis reporting package")
(description
@@ -8104,16 +7937,16 @@ provides reporting features.")
(properties `((upstream-name . "a4Base")))
(build-system r-build-system)
(propagated-inputs
- `(("r-a4core" ,r-a4core)
- ("r-a4preproc" ,r-a4preproc)
- ("r-annaffy" ,r-annaffy)
- ("r-biobase" ,r-biobase)
- ("r-genefilter" ,r-genefilter)
- ("r-glmnet" ,r-glmnet)
- ("r-gplots" ,r-gplots)
- ("r-limma" ,r-limma)
- ("r-mpm" ,r-mpm)
- ("r-multtest" ,r-multtest)))
+ (list r-a4core
+ r-a4preproc
+ r-annaffy
+ r-biobase
+ r-genefilter
+ r-glmnet
+ r-gplots
+ r-limma
+ r-mpm
+ r-multtest))
(home-page "https://bioconductor.org/packages/a4Base/")
(synopsis "Automated Affymetrix array analysis base package")
(description
@@ -8134,11 +7967,7 @@ Affymetrix arrays.")
"0mkgim93441zxhn4wmbin9ydl94srsawis0xwx479l0byj88n07m"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-a4base" ,r-a4base)
- ("r-a4classif" ,r-a4classif)
- ("r-a4core" ,r-a4core)
- ("r-a4preproc" ,r-a4preproc)
- ("r-a4reporting" ,r-a4reporting)))
+ (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
(home-page "https://bioconductor.org/packages/a4/")
(synopsis "Automated Affymetrix array analysis umbrella package")
(description
@@ -8160,28 +7989,28 @@ Affymetrix arrays.")
(properties `((upstream-name . "abseqR")))
(build-system r-build-system)
(inputs
- `(("pandoc" ,pandoc)))
- (propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-biocstyle" ,r-biocstyle)
- ("r-circlize" ,r-circlize)
- ("r-flexdashboard" ,r-flexdashboard)
- ("r-ggcorrplot" ,r-ggcorrplot)
- ("r-ggdendro" ,r-ggdendro)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-knitr" ,r-knitr)
- ("r-plotly" ,r-plotly)
- ("r-plyr" ,r-plyr)
- ("r-png" ,r-png)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape2" ,r-reshape2)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-stringr" ,r-stringr)
- ("r-vegan" ,r-vegan)
- ("r-venndiagram" ,r-venndiagram)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list pandoc))
+ (propagated-inputs
+ (list r-biocparallel
+ r-biocstyle
+ r-circlize
+ r-flexdashboard
+ r-ggcorrplot
+ r-ggdendro
+ r-ggplot2
+ r-gridextra
+ r-knitr
+ r-plotly
+ r-plyr
+ r-png
+ r-rcolorbrewer
+ r-reshape2
+ r-rmarkdown
+ r-stringr
+ r-vegan
+ r-venndiagram))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/malhamdoosh/abseqR")
(synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
(description
@@ -8207,11 +8036,9 @@ further downstream analysis on its output.")
"13dhma34j9ggryainn4x6qvd3hphpxks5gf0mysia00r9hhpwwlc"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-ellipse" ,r-ellipse)
- ("r-ggplot2" ,r-ggplot2)))
+ (list r-biocparallel r-ellipse r-ggplot2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/bacon/")
(synopsis "Controlling bias and inflation in association studies")
(description
@@ -8235,11 +8062,7 @@ fitting a three-component normal mixture on z-scores.")
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-seqlogo" ,r-seqlogo)))
+ (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
(home-page "https://bioconductor.org/packages/rGADEM/")
(synopsis "De novo sequence motif discovery")
(description
@@ -8261,15 +8084,15 @@ genomic sequence data.")
(properties `((upstream-name . "MotIV")))
(build-system r-build-system)
(inputs
- `(("gsl" ,gsl)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-rgadem" ,r-rgadem)
- ("r-s4vectors" ,r-s4vectors)))
+ (list gsl))
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biostrings
+ r-genomicranges
+ r-iranges
+ r-lattice
+ r-rgadem
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/MotIV/")
(synopsis "Motif identification and validation")
(description
@@ -8291,15 +8114,15 @@ distributions, modules and filter motifs.")
(properties `((upstream-name . "MotifDb")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-splitstackshape" ,r-splitstackshape)))
+ (list r-biocgenerics
+ r-biostrings
+ r-genomicranges
+ r-iranges
+ r-rtracklayer
+ r-s4vectors
+ r-splitstackshape))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://www.bioconductor.org/packages/MotifDb/")
(synopsis "Annotated collection of protein-DNA binding sequence motifs")
(description "This package provides more than 2000 annotated position
@@ -8318,26 +8141,26 @@ frequency matrices from nine public sources, for multiple organisms.")
(properties `((upstream-name . "motifbreakR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-grimport" ,r-grimport)
- ("r-gviz" ,r-gviz)
- ("r-iranges" ,r-iranges)
- ("r-matrixstats" ,r-matrixstats)
- ("r-motifdb" ,r-motifdb)
- ("r-motifstack" ,r-motifstack)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tfmpvalue" ,r-tfmpvalue)
- ("r-variantannotation" ,r-variantannotation)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicranges
+ r-grimport
+ r-gviz
+ r-iranges
+ r-matrixstats
+ r-motifdb
+ r-motifstack
+ r-rtracklayer
+ r-s4vectors
+ r-stringr
+ r-summarizedexperiment
+ r-tfmpvalue
+ r-variantannotation))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://www.bioconductor.org/packages/motifbreakR/")
(synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
(description "This package allows biologists to judge in the first place
@@ -8371,13 +8194,9 @@ Bioconductor.")
(properties `((upstream-name . "motifStack")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ade4" ,r-ade4)
- ("r-biostrings" ,r-biostrings)
- ("r-ggplot2" ,r-ggplot2)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-xml" ,r-xml)))
+ (list r-ade4 r-biostrings r-ggplot2 r-htmlwidgets r-xml))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/motifStack/")
(synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
(description
@@ -8402,22 +8221,22 @@ type and symbol colors.")
(properties `((upstream-name . "GenomicScores")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-biobase" ,r-biobase)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biostrings" ,r-biostrings)
- ("r-delayedarray" ,r-delayedarray)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hdf5array" ,r-hdf5array)
- ("r-iranges" ,r-iranges)
- ("r-rhdf5" ,r-rhdf5)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationhub
+ r-biobase
+ r-biocfilecache
+ r-biocgenerics
+ r-biocmanager
+ r-biostrings
+ r-delayedarray
+ r-genomeinfodb
+ r-genomicranges
+ r-hdf5array
+ r-iranges
+ r-rhdf5
+ r-s4vectors
+ r-xml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/rcastelo/GenomicScores/")
(synopsis "Work with genome-wide position-specific scores")
(description
@@ -8439,26 +8258,26 @@ position-specific scores within R and Bioconductor.")
(properties `((upstream-name . "ATACseqQC")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-chippeakanno" ,r-chippeakanno)
- ("r-edger" ,r-edger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-genomicscores" ,r-genomicscores)
- ("r-iranges" ,r-iranges)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-limma" ,r-limma)
- ("r-motifstack" ,r-motifstack)
- ("r-preseqr" ,r-preseqr)
- ("r-randomforest" ,r-randomforest)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-bsgenome
+ r-chippeakanno
+ r-edger
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-genomicscores
+ r-iranges
+ r-kernsmooth
+ r-limma
+ r-motifstack
+ r-preseqr
+ r-randomforest
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ATACseqQC/")
(synopsis "ATAC-seq quality control")
(description
@@ -8486,15 +8305,15 @@ footprints.")
(properties `((upstream-name . "GOfuncR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-mapplots" ,r-mapplots)
- ("r-rcpp" ,r-rcpp)
- ("r-vioplot" ,r-vioplot)))
+ (list r-annotationdbi
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-mapplots
+ r-rcpp
+ r-vioplot))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GOfuncR/")
(synopsis "Gene ontology enrichment using FUNC")
(description
@@ -8535,14 +8354,14 @@ annotations and ontologies.")
(properties `((upstream-name . "ABAEnrichment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abadata" ,r-abadata)
- ("r-data-table" ,r-data-table)
- ("r-gofuncr" ,r-gofuncr)
- ("r-gplots" ,r-gplots)
- ("r-gtools" ,r-gtools)
- ("r-rcpp" ,r-rcpp)))
+ (list r-abadata
+ r-data-table
+ r-gofuncr
+ r-gplots
+ r-gtools
+ r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ABAEnrichment/")
(synopsis "Gene expression enrichment in human brain regions")
(description
@@ -8568,8 +8387,7 @@ the brain using an ontology, both provided by the Allen Brain Atlas project.")
`((upstream-name . "AnnotationFuncs")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dbi" ,r-dbi)))
+ (list r-annotationdbi r-dbi))
(home-page "https://www.iysik.com/r/annotationfuncs")
(synopsis "Annotation translation functions")
(description
@@ -8592,7 +8410,7 @@ different identifieres using the Biocore Data Team data-packages (e.g.
(properties
`((upstream-name . "annotationTools")))
(build-system r-build-system)
- (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (propagated-inputs (list r-biobase))
(home-page "https://bioconductor.org/packages/annotationTools/")
(synopsis "Annotate microarrays and perform gene expression analyses")
(description
@@ -8618,27 +8436,27 @@ text files).")
`((upstream-name . "AllelicImbalance")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gridextra" ,r-gridextra)
- ("r-gviz" ,r-gviz)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-nlme" ,r-nlme)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqinr" ,r-seqinr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biocgenerics
+ r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-gridextra
+ r-gviz
+ r-iranges
+ r-lattice
+ r-latticeextra
+ r-nlme
+ r-rsamtools
+ r-s4vectors
+ r-seqinr
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/pappewaio/AllelicImbalance")
(synopsis "Investigate allele-specific expression")
(description
@@ -8660,16 +8478,16 @@ investigation using RNA-seq data.")
(properties `((upstream-name . "AUCell")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-gseabase" ,r-gseabase)
- ("r-mixtools" ,r-mixtools)
- ("r-r-utils" ,r-r-utils)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocgenerics
+ r-data-table
+ r-gseabase
+ r-mixtools
+ r-r-utils
+ r-s4vectors
+ r-shiny
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/AUCell/")
(synopsis "Analysis of gene set activity in single-cell RNA-seq data")
(description
@@ -8699,18 +8517,18 @@ needed.")
(properties `((upstream-name . "EBImage")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-fftwtools" ,r-fftwtools)
- ("r-htmltools" ,r-htmltools)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-jpeg" ,r-jpeg)
- ("r-locfit" ,r-locfit)
- ("r-png" ,r-png)
- ("r-rcurl" ,r-rcurl)
- ("r-tiff" ,r-tiff)))
+ (list r-abind
+ r-biocgenerics
+ r-fftwtools
+ r-htmltools
+ r-htmlwidgets
+ r-jpeg
+ r-locfit
+ r-png
+ r-rcurl
+ r-tiff))
(native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
+ (list r-knitr)) ; for vignettes
(home-page "https://github.com/aoles/EBImage")
(synopsis "Image processing and analysis toolbox for R")
(description
@@ -8737,18 +8555,17 @@ visualization with image data.")
"141hbryifm6na5shjyrbjwwksqnl75kqp1m2zl03l9sjqm0kapab"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-ebimage" ,r-ebimage)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-matrix" ,r-matrix)
- ("r-mzr" ,r-mzr)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment"
- ,r-summarizedexperiment)))
+ (list r-biocgenerics
+ r-data-table
+ r-ebimage
+ r-iranges
+ r-limma
+ r-matrix
+ r-mzr
+ r-s4vectors
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/hansenlab/yamss")
(synopsis "Tools for high-throughput metabolomics")
(description
@@ -8771,12 +8588,9 @@ analysis.")
"0q2lyb8p1xhqqhw4q1br4r8mwq06mjws8iwbbilkngvs3brbmrzl"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-circlize" ,r-circlize)
- ("r-genomicranges" ,r-genomicranges)
- ("r-getoptlong" ,r-getoptlong)
- ("r-iranges" ,r-iranges)))
+ (list r-circlize r-genomicranges r-getoptlong r-iranges))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/jokergoo/gtrellis")
(synopsis "Genome level Trellis layout")
(description
@@ -8802,21 +8616,21 @@ genomic categories and to add self-defined graphics in the plot.")
`((upstream-name . "SomaticSignatures")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-nmf" ,r-nmf)
- ("r-pcamethods" ,r-pcamethods)
- ("r-proxy" ,r-proxy)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biostrings
+ r-genomeinfodb
+ r-genomicranges
+ r-ggbio
+ r-ggplot2
+ r-iranges
+ r-nmf
+ r-pcamethods
+ r-proxy
+ r-reshape2
+ r-s4vectors
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/juliangehring/SomaticSignatures")
(synopsis "Somatic signatures")
(description
@@ -8840,31 +8654,31 @@ decomposition algorithms.")
(properties `((upstream-name . "YAPSA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-circlize" ,r-circlize)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-corrplot" ,r-corrplot)
- ("r-dendextend" ,r-dendextend)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-getoptlong" ,r-getoptlong)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-gtrellis" ,r-gtrellis)
- ("r-keggrest" ,r-keggrest)
- ("r-limsolve" ,r-limsolve)
- ("r-magrittr" ,r-magrittr)
- ("r-pmcmr" ,r-pmcmr)
- ("r-pracma" ,r-pracma)
- ("r-reshape2" ,r-reshape2)
- ("r-somaticsignatures" ,r-somaticsignatures)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biostrings
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-circlize
+ r-complexheatmap
+ r-corrplot
+ r-dendextend
+ r-doparallel
+ r-dplyr
+ r-genomeinfodb
+ r-genomicranges
+ r-getoptlong
+ r-ggbeeswarm
+ r-ggplot2
+ r-gridextra
+ r-gtrellis
+ r-keggrest
+ r-limsolve
+ r-magrittr
+ r-pmcmr
+ r-pracma
+ r-reshape2
+ r-somaticsignatures
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/YAPSA/")
(synopsis "Yet another package for signature analysis")
(description
@@ -8888,12 +8702,12 @@ provided.")
"0h7dl4if6skbcqdjdzqyghyswhwpx7xvb54lffz4wdaxpabp3001"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-affyio" ,r-affyio)
- ("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biostrings" ,r-biostrings)
- ("r-xvector" ,r-xvector)))
+ (list r-affy
+ r-affyio
+ r-biobase
+ r-biocmanager
+ r-biostrings
+ r-xvector))
(home-page "https://bioconductor.org/packages/gcrma/")
(synopsis "Background adjustment using sequence information")
(description
@@ -8924,11 +8738,7 @@ gene-specific binding is expected.")
"04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-gcrma" ,r-gcrma)
- ("r-genefilter" ,r-genefilter)))
+ (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
(home-page "https://bioconductor.org/packages/simpleaffy/")
(synopsis "Very simple high level analysis of Affymetrix data")
(description
@@ -8952,7 +8762,7 @@ generating high resolution journal figures.")
"18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-simpleaffy" ,r-simpleaffy)))
+ (list r-simpleaffy))
(home-page "https://bioconductor.org/packages/yaqcaffy/")
(synopsis "Affymetrix quality control and reproducibility analysis")
(description
@@ -8974,15 +8784,15 @@ chips with the MAQC reference datasets.")
"1r2wbsndc0ji22ap27gbr1wy8icj3cjxwqlz1x0gvxkaj69mwsfq"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iterators" ,r-iterators)
- ("r-minfi" ,r-minfi)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-biobase
+ r-doparallel
+ r-foreach
+ r-ggplot2
+ r-iterators
+ r-minfi
+ r-rcolorbrewer))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/quantro/")
(synopsis "Test for when to use quantile normalization")
(description
@@ -9007,19 +8817,19 @@ groups.")
"0nk4qzrwjiv8q39lgil9x25bm3gpzrnhd37d7754kpxhs2fsmw9d"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biomart" ,r-biomart)
- ("r-downloader" ,r-downloader)
- ("r-edger" ,r-edger)
- ("r-gplots" ,r-gplots)
- ("r-limma" ,r-limma)
- ("r-matrixstats" ,r-matrixstats)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-quantro" ,r-quantro)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-readr" ,r-readr)))
+ (list r-biobase
+ r-biomart
+ r-downloader
+ r-edger
+ r-gplots
+ r-limma
+ r-matrixstats
+ r-preprocesscore
+ r-quantro
+ r-rcolorbrewer
+ r-readr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/yarn/")
(synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
(description
@@ -9044,14 +8854,14 @@ large RNA-seq experiments.")
"0hqh4vsnxl2sn1bf6s6wxl2nskb40rhvrysdvb6dr60zkih3g347"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocgenerics
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-rtracklayer
+ r-s4vectors
+ r-summarizedexperiment))
(home-page "https://github.com/vodkatad/roar/")
(synopsis "Identify differential APA usage from RNA-seq alignments")
(description
@@ -9074,17 +8884,17 @@ sites and alignments obtained from standard RNA-seq experiments.")
(properties `((upstream-name . "XBSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-ggplot2" ,r-ggplot2)
- ("r-locfit" ,r-locfit)
- ("r-magrittr" ,r-magrittr)
- ("r-matrixstats" ,r-matrixstats)
- ("r-pracma" ,r-pracma)
- ("r-roar" ,r-roar)))
+ (list r-biobase
+ r-deseq2
+ r-dplyr
+ r-ggplot2
+ r-locfit
+ r-magrittr
+ r-matrixstats
+ r-pracma
+ r-roar))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/Liuy12/XBSeq")
(synopsis "Test for differential expression for RNA-seq data")
(description
@@ -9114,7 +8924,7 @@ genes.")
`((upstream-name . "MassSpecWavelet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-waveslim" ,r-waveslim)))
+ (list r-waveslim))
(home-page "https://bioconductor.org/packages/MassSpecWavelet/")
(synopsis "Mass spectrum processing by wavelet-based algorithms")
(description
@@ -9136,25 +8946,25 @@ based on @dfn{Continuous Wavelet Transform} (CWT).")
"19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-massspecwavelet" ,r-massspecwavelet)
- ("r-mscoreutils" ,r-mscoreutils)
- ("r-msfeatures" ,r-msfeatures)
- ("r-msnbase" ,r-msnbase)
- ("r-mzr" ,r-mzr)
- ("r-plyr" ,r-plyr)
- ("r-protgenerics" ,r-protgenerics)
- ("r-rann" ,r-rann)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-robustbase" ,r-robustbase)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-iranges
+ r-lattice
+ r-massspecwavelet
+ r-mscoreutils
+ r-msfeatures
+ r-msnbase
+ r-mzr
+ r-plyr
+ r-protgenerics
+ r-rann
+ r-rcolorbrewer
+ r-robustbase
+ r-s4vectors
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/xcms/")
(synopsis "LC/MS and GC/MS mass spectrometry data analysis")
(description
@@ -9178,11 +8988,9 @@ data for high-throughput, untargeted analyte profiling.")
(properties `((upstream-name . "Wrench")))
(build-system r-build-system)
(propagated-inputs
- `(("r-limma" ,r-limma)
- ("r-locfit" ,r-locfit)
- ("r-matrixstats" ,r-matrixstats)))
+ (list r-limma r-locfit r-matrixstats))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/HCBravoLab/Wrench")
(synopsis "Wrench normalization for sparse count data")
(description
@@ -9203,18 +9011,18 @@ that arising from 16s metagenomic surveys.")
"01y1rbmxjza7qx3q33k0r241if69hzkx9plgmj59wyji22lm7syi"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-cowplot" ,r-cowplot)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-purrr" ,r-purrr)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-assertthat
+ r-cowplot
+ r-dplyr
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-purrr
+ r-rtracklayer
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/wiggleplotr/")
(synopsis "Make read coverage plots from BigWig files")
(description
@@ -9258,17 +9066,16 @@ widgets in R.")
"1r3rjvfhqbbzdhlslnc86kr2iip3xgvr81zpvcr8xv9mysgrln17"))))
(build-system r-build-system)
(inputs
- `(("netpbm" ,netpbm)
- ("perl" ,perl)))
- (propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-annaffy" ,r-annaffy)
- ("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-gcrma" ,r-gcrma)
- ("r-multtest" ,r-multtest)
- ("r-qvalue" ,r-qvalue)
- ("r-vsn" ,r-vsn)))
+ (list netpbm perl))
+ (propagated-inputs
+ (list r-affy
+ r-annaffy
+ r-biobase
+ r-biocmanager
+ r-gcrma
+ r-multtest
+ r-qvalue
+ r-vsn))
(home-page "https://www.bioconductor.org/")
(synopsis "Bioconductor web interface")
(description
@@ -9291,15 +9098,15 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
"05w95bnq63a339d8x4932k81ycqf825s3qwn98vr52v5g2hv46fq"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-edger" ,r-edger)
- ("r-genefilter" ,r-genefilter)
- ("r-matrix" ,r-matrix)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-softimpute" ,r-softimpute)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocparallel
+ r-edger
+ r-genefilter
+ r-matrix
+ r-singlecellexperiment
+ r-softimpute
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/zinbwave")
(synopsis "Zero-inflated negative binomial model for RNA-seq data")
(description "This package implements a general and flexible zero-inflated
@@ -9325,13 +9132,9 @@ the data.")
(properties `((upstream-name . "zFPKM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-checkmate" ,r-checkmate)
- ("r-dplyr" ,r-dplyr)
- ("r-ggplot2" ,r-ggplot2)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tidyr" ,r-tidyr)))
+ (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/ronammar/zFPKM/")
(synopsis "Functions to facilitate zFPKM transformations")
(description
@@ -9354,13 +9157,11 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
(properties `((upstream-name . "Rbowtie2")))
(build-system r-build-system)
(propagated-inputs
- `(("r-magrittr" ,r-magrittr)
- ("r-rsamtools" ,r-rsamtools)))
+ (list r-magrittr r-rsamtools))
(inputs
- `(("samtools" ,samtools)
- ("zlib" ,zlib)))
+ (list samtools zlib))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/Rbowtie2/")
(synopsis "R wrapper for Bowtie2 and AdapterRemoval")
(description
@@ -9382,14 +9183,14 @@ rapid adapter trimming, identification, and read merging.")
"0zhr5i5v87akzqjb6wid67nhg2icrw6w0awdy87x848c6c1i6j9y"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-dplyr" ,r-dplyr)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gridextra" ,r-gridextra)
- ("r-tidyr" ,r-tidyr)))
+ (list r-biobase
+ r-dplyr
+ r-ggplot2
+ r-ggrepel
+ r-gridextra
+ r-tidyr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/saezlab/progeny")
(synopsis "Pathway responsive gene activity inference")
(description
@@ -9413,7 +9214,7 @@ expression\".")
(properties
`((upstream-name . "ARRmNormalization")))
(build-system r-build-system)
- (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
+ (propagated-inputs (list r-arrmdata))
(home-page "https://bioconductor.org/packages/ARRmNormalization/")
(synopsis "Adaptive robust regression normalization for methylation data")
(description
@@ -9436,16 +9237,16 @@ Infinium HumanMethylation 450k assay.")
(properties `((upstream-name . "BiocFileCache")))
(build-system r-build-system)
(propagated-inputs
- `(("r-curl" ,r-curl)
- ("r-dbi" ,r-dbi)
- ("r-dbplyr" ,r-dbplyr)
- ("r-dplyr" ,r-dplyr)
- ("r-filelock" ,r-filelock)
- ("r-httr" ,r-httr)
- ("r-rappdirs" ,r-rappdirs)
- ("r-rsqlite" ,r-rsqlite)))
+ (list r-curl
+ r-dbi
+ r-dbplyr
+ r-dplyr
+ r-filelock
+ r-httr
+ r-rappdirs
+ r-rsqlite))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocFileCache/")
(synopsis "Manage files across sessions")
(description
@@ -9468,7 +9269,7 @@ and data files used across sessions.")
"0w6r2clk8wdnnnjmq3cspmxiq1c8vwprd66xmdrhcqzbjkpkdw2b"))))
(properties `((upstream-name . "iClusterPlus")))
(build-system r-build-system)
- (native-inputs `(("gfortran" ,gfortran)))
+ (native-inputs (list gfortran))
(home-page "https://bioconductor.org/packages/iClusterPlus/")
(synopsis "Integrative clustering of multi-type genomic data")
(description
@@ -9499,7 +9300,7 @@ Gaussian distributions.")
(properties `((upstream-name . "Rbowtie")))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/Rbowtie/")
(synopsis "R bowtie wrapper")
(description
@@ -9522,22 +9323,22 @@ alignment tool.")
(properties `((upstream-name . "SGSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-runit" ,r-runit)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biocgenerics
+ r-biostrings
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-igraph
+ r-iranges
+ r-rsamtools
+ r-rtracklayer
+ r-runit
+ r-s4vectors
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/SGSeq/")
(synopsis "Splice event prediction and quantification from RNA-seq data")
(description
@@ -9577,11 +9378,9 @@ interpretation.")
(("^CPP =.*") (which "g++")))
#t)))))
(propagated-inputs
- `(("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-sgseq" ,r-sgseq)))
+ (list r-genomicfeatures r-genomicranges r-sgseq))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/fmicompbio/Rhisat2")
(synopsis "R Wrapper for HISAT2 sequence aligner")
(description
@@ -9605,25 +9404,25 @@ index.")
(properties `((upstream-name . "QuasR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-rbowtie" ,r-rbowtie)
- ("r-rhtslib" ,r-rhtslib)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shortread" ,r-shortread)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicfiles
+ r-genomicranges
+ r-iranges
+ r-rbowtie
+ r-rhtslib
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-shortread))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/QuasR/")
(synopsis "Quantify and annotate short reads in R")
(description
@@ -9647,26 +9446,26 @@ quantification of genomic regions of interest.")
(properties `((upstream-name . "Rqc")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocstyle" ,r-biocstyle)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-knitr" ,r-knitr)
- ("r-markdown" ,r-markdown)
- ("r-plyr" ,r-plyr)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-shortread" ,r-shortread)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biocstyle
+ r-biostrings
+ r-biovizbase
+ r-genomicalignments
+ r-genomicfiles
+ r-ggplot2
+ r-iranges
+ r-knitr
+ r-markdown
+ r-plyr
+ r-rcpp
+ r-reshape2
+ r-rsamtools
+ r-s4vectors
+ r-shiny
+ r-shortread))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/labbcb/Rqc")
(synopsis "Quality control tool for high-throughput sequencing data")
(description
@@ -9690,10 +9489,7 @@ graphics.")
(properties `((upstream-name . "BiRewire")))
(build-system r-build-system)
(propagated-inputs
- `(("r-igraph" ,r-igraph)
- ("r-matrix" ,r-matrix)
- ("r-slam" ,r-slam)
- ("r-tsne" ,r-tsne)))
+ (list r-igraph r-matrix r-slam r-tsne))
(home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
(synopsis "Tools for randomization of bipartite graphs")
(description
@@ -9718,9 +9514,7 @@ routines to analyse the resulting networks and their natural projections.")
"00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-limma" ,r-limma)
- ("r-mass" ,r-mass)))
+ (list r-biobase r-limma r-mass))
(home-page "https://bioconductor.org/packages/birta")
(synopsis "Bayesian inference of regulation of transcriptional activity")
(description
@@ -9748,18 +9542,18 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.")
(properties `((upstream-name . "MultiDataSet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-qqman" ,r-qqman)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biobase
+ r-biocgenerics
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-iranges
+ r-limma
+ r-qqman
+ r-s4vectors
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/MultiDataSet/")
(synopsis "Implementation of MultiDataSet and ResultSet")
(description
@@ -9784,10 +9578,9 @@ packages.")
"0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-multidataset" ,r-multidataset)))
+ (list r-biobase r-multidataset))
(native-inputs
- `(("r-knitr" ,r-knitr))) ; for vignettes
+ (list r-knitr)) ; for vignettes
(home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
(synopsis "Multivariate analysis and feature selection of omics data")
(description
@@ -9822,13 +9615,9 @@ coefficients).")
"189018qahyw33dmg73wa7k4rp8nzrx6ai8f2dr6vhbpcdc1gnm0z"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-e1071" ,r-e1071)
- ("r-multidataset" ,r-multidataset)
- ("r-randomforest" ,r-randomforest)
- ("r-ropls" ,r-ropls)))
+ (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/biosigner/")
(synopsis "Signature discovery from omics data")
(description
@@ -9855,21 +9644,21 @@ datasets.")
"1ha2wn56cdab4p3wdwv4xlqjsgl7sd8phbx71qbclrbdwpq2mi7i"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-dplyr" ,r-dplyr)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-readr" ,r-readr)
- ("r-regioner" ,r-regioner)
- ("r-reshape2" ,r-reshape2)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationhub
+ r-dplyr
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-readr
+ r-regioner
+ r-reshape2
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/annotatr/")
(synopsis "Annotation of genomic regions to genomic annotations")
(description
@@ -9896,9 +9685,9 @@ annotations.")
"0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(propagated-inputs
- `(("r-matrix" ,r-matrix)))
+ (list r-matrix))
(home-page "https://bioconductor.org/packages/Rsubread/")
(synopsis "Subread sequence alignment and counting for R")
(description
@@ -9923,12 +9712,12 @@ and to both short and long sequence reads.")
(properties `((upstream-name . "flowUtils")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-corpcor" ,r-corpcor)
- ("r-flowcore" ,r-flowcore)
- ("r-graph" ,r-graph)
- ("r-runit" ,r-runit)
- ("r-xml" ,r-xml)))
+ (list r-biobase
+ r-corpcor
+ r-flowcore
+ r-graph
+ r-runit
+ r-xml))
(home-page "https://github.com/jspidlen/flowUtils")
(synopsis "Utilities for flow cytometry")
(description
@@ -9950,9 +9739,7 @@ and to both short and long sequence reads.")
`((upstream-name . "ConsensusClusterPlus")))
(build-system r-build-system)
(propagated-inputs
- `(("r-all" ,r-all)
- ("r-biobase" ,r-biobase)
- ("r-cluster" ,r-cluster)))
+ (list r-all r-biobase r-cluster))
(home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
(synopsis "Clustering algorithm")
(description
@@ -9974,14 +9761,14 @@ cluster count and membership by stability evidence in unsupervised analysis.")
(properties `((upstream-name . "cytolib")))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rcppparallel" ,r-rcppparallel)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-rprotobuflib" ,r-rprotobuflib)))
+ (list r-bh
+ r-rcpp
+ r-rcpparmadillo
+ r-rcppparallel
+ r-rhdf5lib
+ r-rprotobuflib))
(home-page "https://bioconductor.org/packages/cytolib/")
(synopsis "C++ infrastructure for working with gated cytometry")
(description
@@ -10003,17 +9790,17 @@ interact with gated cytometry data.")
(properties `((upstream-name . "flowCore")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-cytolib" ,r-cytolib)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rprotobuflib" ,r-rprotobuflib)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-bh
+ r-biobase
+ r-biocgenerics
+ r-cytolib
+ r-matrixstats
+ r-rcpp
+ r-rcpparmadillo
+ r-rprotobuflib
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/flowCore")
(synopsis "Basic structures for flow cytometry data")
(description
@@ -10035,10 +9822,7 @@ with flow cytometry data.")
(properties `((upstream-name . "flowMeans")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-feature" ,r-feature)
- ("r-flowcore" ,r-flowcore)
- ("r-rrcov" ,r-rrcov)))
+ (list r-biobase r-feature r-flowcore r-rrcov))
(home-page "https://bioconductor.org/packages/flowMeans")
(synopsis "Non-parametric flow cytometry data gating")
(description
@@ -10061,16 +9845,16 @@ change point detection.")
(properties `((upstream-name . "ncdfFlow")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-flowcore" ,r-flowcore)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list r-bh
+ r-biobase
+ r-biocgenerics
+ r-flowcore
+ r-rcpp
+ r-rcpparmadillo
+ r-rhdf5lib
+ r-zlibbioc))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ncdfFlow/")
(synopsis "HDF5 based storage for flow cytometry data")
(description
@@ -10092,19 +9876,19 @@ manipulation of flow cytometry data.")
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-flowcore" ,r-flowcore)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-hexbin" ,r-hexbin)
- ("r-ncdfflow" ,r-ncdfflow)
- ("r-plyr" ,r-plyr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-scales" ,r-scales)))
+ (list r-data-table
+ r-flowcore
+ r-flowworkspace
+ r-ggplot2
+ r-gridextra
+ r-hexbin
+ r-ncdfflow
+ r-plyr
+ r-rcolorbrewer
+ r-rlang
+ r-scales))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/RGLab/ggcyto/issues")
(synopsis "Visualize Cytometry data with ggplot")
(description
@@ -10129,17 +9913,17 @@ statistics to the plot.")
(properties `((upstream-name . "flowViz")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-flowcore" ,r-flowcore)
- ("r-hexbin" ,r-hexbin)
- ("r-idpmisc" ,r-idpmisc)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-mass" ,r-mass)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-biobase
+ r-flowcore
+ r-hexbin
+ r-idpmisc
+ r-kernsmooth
+ r-lattice
+ r-latticeextra
+ r-mass
+ r-rcolorbrewer))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/flowViz/")
(synopsis "Visualization for flow cytometry")
(description
@@ -10163,20 +9947,19 @@ statistics to the plot.")
`(#:configure-flags
(list "--configure-args=--enable-bundled-gsl=no")))
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-clue" ,r-clue)
- ("r-corpcor" ,r-corpcor)
- ("r-ellipse" ,r-ellipse)
- ("r-flowcore" ,r-flowcore)
- ("r-flowviz" ,r-flowviz)
- ("r-graph" ,r-graph)
- ("r-mnormt" ,r-mnormt)))
+ (list r-biobase
+ r-biocgenerics
+ r-clue
+ r-corpcor
+ r-ellipse
+ r-flowcore
+ r-flowviz
+ r-graph
+ r-mnormt))
(inputs
- `(("gsl" ,gsl)))
+ (list gsl))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("r-knitr" ,r-knitr)))
+ (list pkg-config r-knitr))
(home-page "https://bioconductor.org/packages/flowClust")
(synopsis "Clustering for flow cytometry")
(description
@@ -10207,7 +9990,7 @@ model with Box-Cox transformation.")
(with-directory-excursion "src"
(invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/RProtoBufLib/")
(synopsis "C++ headers and static libraries of Protocol buffers")
(description
@@ -10229,35 +10012,35 @@ for other R packages to compile and link against.")
(properties `((upstream-name . "flowWorkspace")))
(build-system r-build-system)
(propagated-inputs
- `(("r-aws-s3" ,r-aws-s3)
- ("r-aws-signature" ,r-aws-signature)
- ("r-bh" ,r-bh)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-cytolib" ,r-cytolib)
- ("r-data-table" ,r-data-table)
- ("r-delayedarray" ,r-delayedarray)
- ("r-digest" ,r-digest)
- ("r-dplyr" ,r-dplyr)
- ("r-flowcore" ,r-flowcore)
- ("r-ggplot2" ,r-ggplot2)
- ("r-graph" ,r-graph)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-matrixstats" ,r-matrixstats)
- ("r-ncdfflow" ,r-ncdfflow)
- ("r-rbgl" ,r-rbgl)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rcppparallel" ,r-rcppparallel)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-rprotobuflib" ,r-rprotobuflib)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-aws-s3
+ r-aws-signature
+ r-bh
+ r-biobase
+ r-biocgenerics
+ r-cytolib
+ r-data-table
+ r-delayedarray
+ r-digest
+ r-dplyr
+ r-flowcore
+ r-ggplot2
+ r-graph
+ r-lattice
+ r-latticeextra
+ r-matrixstats
+ r-ncdfflow
+ r-rbgl
+ r-rcpp
+ r-rcpparmadillo
+ r-rcppparallel
+ r-rgraphviz
+ r-rhdf5lib
+ r-rprotobuflib
+ r-s4vectors
+ r-scales
+ r-xml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/flowWorkspace/")
(synopsis "Infrastructure for working with cytometry data")
(description
@@ -10283,20 +10066,20 @@ matches the flowJo analysis.")
(properties `((upstream-name . "flowStats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-cluster" ,r-cluster)
- ("r-fda" ,r-fda)
- ("r-flowcore" ,r-flowcore)
- ("r-flowviz" ,r-flowviz)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-ks" ,r-ks)
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-ncdfflow" ,r-ncdfflow)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rrcov" ,r-rrcov)))
+ (list r-biobase
+ r-biocgenerics
+ r-cluster
+ r-fda
+ r-flowcore
+ r-flowviz
+ r-flowworkspace
+ r-kernsmooth
+ r-ks
+ r-lattice
+ r-mass
+ r-ncdfflow
+ r-rcolorbrewer
+ r-rrcov))
(home-page "http://www.github.com/RGLab/flowStats")
(synopsis "Statistical methods for the analysis of flow cytometry data")
(description
@@ -10319,29 +10102,29 @@ package.")
(properties `((upstream-name . "openCyto")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-clue" ,r-clue)
- ("r-data-table" ,r-data-table)
- ("r-flowclust" ,r-flowclust)
- ("r-flowcore" ,r-flowcore)
- ("r-flowstats" ,r-flowstats)
- ("r-flowviz" ,r-flowviz)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-graph" ,r-graph)
- ("r-gtools" ,r-gtools)
- ("r-ks" ,r-ks)
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-ncdfflow" ,r-ncdfflow)
- ("r-plyr" ,r-plyr)
- ("r-r-utils" ,r-r-utils)
- ("r-rbgl" ,r-rbgl)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rrcov" ,r-rrcov)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-clue
+ r-data-table
+ r-flowclust
+ r-flowcore
+ r-flowstats
+ r-flowviz
+ r-flowworkspace
+ r-graph
+ r-gtools
+ r-ks
+ r-lattice
+ r-mass
+ r-ncdfflow
+ r-plyr
+ r-r-utils
+ r-rbgl
+ r-rcolorbrewer
+ r-rcpp
+ r-rrcov))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/openCyto")
(synopsis "Hierarchical gating pipeline for flow cytometry data")
(description
@@ -10363,38 +10146,37 @@ sequential way to mimic the manual gating strategy.")
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
- `(("libxml2" ,libxml2)
- ("zlib" ,zlib)))
- (propagated-inputs
- `(("r-base64enc" ,r-base64enc)
- ("r-bh" ,r-bh)
- ("r-biobase" ,r-biobase)
- ("r-corpcor" ,r-corpcor)
- ("r-cytolib" ,r-cytolib)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-flowcore" ,r-flowcore)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-ggcyto" ,r-ggcyto)
- ("r-graph" ,r-graph)
- ("r-jsonlite" ,r-jsonlite)
- ("r-lattice" ,r-lattice)
- ("r-opencyto" ,r-opencyto)
- ("r-plyr" ,r-plyr)
- ("r-rbgl" ,r-rbgl)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rcppparallel" ,r-rcppparallel)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-rprotobuflib" ,r-rprotobuflib)
- ("r-runit" ,r-runit)
- ("r-tibble" ,r-tibble)
- ("r-xml" ,r-xml)
- ("r-xml2" ,r-xml2)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list libxml2 zlib))
+ (propagated-inputs
+ (list r-base64enc
+ r-bh
+ r-biobase
+ r-corpcor
+ r-cytolib
+ r-data-table
+ r-dplyr
+ r-flowcore
+ r-flowworkspace
+ r-ggcyto
+ r-graph
+ r-jsonlite
+ r-lattice
+ r-opencyto
+ r-plyr
+ r-rbgl
+ r-rcpp
+ r-rcpparmadillo
+ r-rcppparallel
+ r-rgraphviz
+ r-rhdf5lib
+ r-rprotobuflib
+ r-runit
+ r-tibble
+ r-xml
+ r-xml2
+ r-yaml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/RGLab/CytoML")
(synopsis "GatingML interface for cross platform cytometry data sharing")
(description
@@ -10416,28 +10198,28 @@ standard to exchange gated cytometry data with other software platforms.")
(properties `((upstream-name . "FlowSOM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-colorramps" ,r-colorramps)
- ("r-consensusclusterplus" ,r-consensusclusterplus)
- ("r-cytoml" ,r-cytoml)
- ("r-dplyr" ,r-dplyr)
- ("r-flowcore" ,r-flowcore)
- ("r-flowworkspace" ,r-flowworkspace)
- ("r-ggforce" ,r-ggforce)
- ("r-ggnewscale" ,r-ggnewscale)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggpointdensity" ,r-ggpointdensity)
- ("r-ggpubr" ,r-ggpubr)
- ("r-ggrepel" ,r-ggrepel)
- ("r-igraph" ,r-igraph)
- ("r-magrittr" ,r-magrittr)
- ("r-pheatmap" ,r-pheatmap)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-rtsne" ,r-rtsne)
- ("r-scattermore" ,r-scattermore)
- ("r-tidyr" ,r-tidyr)
- ("r-xml" ,r-xml)))
+ (list r-biocgenerics
+ r-colorramps
+ r-consensusclusterplus
+ r-cytoml
+ r-dplyr
+ r-flowcore
+ r-flowworkspace
+ r-ggforce
+ r-ggnewscale
+ r-ggplot2
+ r-ggpointdensity
+ r-ggpubr
+ r-ggrepel
+ r-igraph
+ r-magrittr
+ r-pheatmap
+ r-rcolorbrewer
+ r-rlang
+ r-rtsne
+ r-scattermore
+ r-tidyr
+ r-xml))
(home-page "https://bioconductor.org/packages/FlowSOM/")
(synopsis "Visualize and interpret cytometry data")
(description
@@ -10459,23 +10241,23 @@ self-organizing map clustering and minimal spanning trees.")
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-corpcor" ,r-corpcor)
- ("r-dplyr" ,r-dplyr)
- ("r-ellipse" ,r-ellipse)
- ("r-ggrepel" ,r-ggrepel)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-igraph" ,r-igraph)
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rarpack" ,r-rarpack)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape2" ,r-reshape2)
- ("r-tidyr" ,r-tidyr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocparallel
+ r-corpcor
+ r-dplyr
+ r-ellipse
+ r-ggrepel
+ r-ggplot2
+ r-gridextra
+ r-igraph
+ r-lattice
+ r-mass
+ r-matrixstats
+ r-rarpack
+ r-rcolorbrewer
+ r-reshape2
+ r-tidyr))
+ (native-inputs
+ (list r-knitr))
(home-page "http://www.mixOmics.org")
(synopsis "Multivariate methods for exploration of biological datasets")
(description
@@ -10505,25 +10287,25 @@ delete entire rows with missing data.")
(properties `((upstream-name . "DepecheR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beanplot" ,r-beanplot)
- ("r-dosnow" ,r-dosnow)
- ("r-dplyr" ,r-dplyr)
- ("r-fnn" ,r-fnn)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gmodels" ,r-gmodels)
- ("r-gplots" ,r-gplots)
- ("r-mass" ,r-mass)
- ("r-matrixstats" ,r-matrixstats)
- ("r-mixomics" ,r-mixomics)
- ("r-moments" ,r-moments)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-reshape2" ,r-reshape2)
- ("r-robustbase" ,r-robustbase)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-beanplot
+ r-dosnow
+ r-dplyr
+ r-fnn
+ r-foreach
+ r-ggplot2
+ r-gmodels
+ r-gplots
+ r-mass
+ r-matrixstats
+ r-mixomics
+ r-moments
+ r-rcpp
+ r-rcppeigen
+ r-reshape2
+ r-robustbase
+ r-viridis))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/DepecheR/")
(synopsis "Identify traits of clusters in high-dimensional entities")
(description
@@ -10551,20 +10333,20 @@ data, to only emphasize the data that actually matters.")
(properties `((upstream-name . "RcisTarget")))
(build-system r-build-system)
(propagated-inputs
- `(("r-arrow" ,r-arrow)
- ("r-aucell" ,r-aucell)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-feather" ,r-feather)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gseabase" ,r-gseabase)
- ("r-r-utils" ,r-r-utils)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tibble" ,r-tibble)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-arrow
+ r-aucell
+ r-biocgenerics
+ r-data-table
+ r-dplyr
+ r-feather
+ r-genomeinfodb
+ r-genomicranges
+ r-gseabase
+ r-r-utils
+ r-summarizedexperiment
+ r-tibble))
+ (native-inputs
+ (list r-knitr))
(home-page "https://aertslab.org/#scenic")
(synopsis "Identify transcription factor binding motifs enriched on a gene list")
(description
@@ -10593,12 +10375,8 @@ genes in the gene-set that are ranked above the leading edge).")
(properties `((upstream-name . "Chicago")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-delaporte" ,r-delaporte)
- ("r-hmisc" ,r-hmisc)
- ("r-mass" ,r-mass)
- ("r-matrixstats" ,r-matrixstats)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/Chicago")
(synopsis "Capture Hi-C analysis of genomic organization")
(description
@@ -10618,30 +10396,30 @@ genes in the gene-set that are ranked above the leading edge).")
"1fc69nkm2cwpr6gkfmra2ph0lrmw486chswp4pn8i70ia43fzdm7"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-fnn" ,r-fnn)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-glasso" ,r-glasso)
- ("r-gviz" ,r-gviz)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-monocle" ,r-monocle)
- ("r-plyr" ,r-plyr)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-stringi" ,r-stringi)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-vgam" ,r-vgam)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-assertthat
+ r-biobase
+ r-biocgenerics
+ r-data-table
+ r-dplyr
+ r-fnn
+ r-genomicranges
+ r-ggplot2
+ r-glasso
+ r-gviz
+ r-igraph
+ r-iranges
+ r-matrix
+ r-monocle
+ r-plyr
+ r-reshape2
+ r-s4vectors
+ r-stringi
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-vgam))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/cicero/")
(synopsis "Predict cis-co-accessibility from single-cell data")
(description
@@ -10668,9 +10446,9 @@ accessibility data.")
(base32
"077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
(propagated-inputs
- `(("r-monocle3" ,r-monocle3)
- ,@(alist-delete "r-monocle"
- (package-propagated-inputs r-cicero)))))))
+ (modify-inputs (package-propagated-inputs r-cicero)
+ (delete "r-monocle")
+ (prepend r-monocle3))))))
(define-public r-circrnaprofiler
(package
@@ -10687,31 +10465,31 @@ accessibility data.")
`((upstream-name . "circRNAprofiler")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-edger" ,r-edger)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gwascat" ,r-gwascat)
- ("r-iranges" ,r-iranges)
- ("r-magrittr" ,r-magrittr)
- ("r-r-utils" ,r-r-utils)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqinr" ,r-seqinr)
- ("r-stringi" ,r-stringi)
- ("r-stringr" ,r-stringr)
- ("r-universalmotif" ,r-universalmotif)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationhub
+ r-biostrings
+ r-bsgenome
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-deseq2
+ r-dplyr
+ r-edger
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-gwascat
+ r-iranges
+ r-magrittr
+ r-r-utils
+ r-readr
+ r-reshape2
+ r-rlang
+ r-rtracklayer
+ r-s4vectors
+ r-seqinr
+ r-stringi
+ r-stringr
+ r-universalmotif))
+ (native-inputs
+ (list r-knitr))
(home-page
"https://github.com/Aufiero/circRNAprofiler")
(synopsis
@@ -10741,21 +10519,21 @@ analysis, evolutionary conservation, biogenesis to functional analysis.")
"0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-aucell" ,r-aucell)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-dosnow" ,r-dosnow)
- ("r-dt" ,r-dt)
- ("r-feather" ,r-feather)
- ("r-fitdistrplus" ,r-fitdistrplus)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-lda" ,r-lda)
- ("r-matrix" ,r-matrix)
- ("r-plyr" ,r-plyr)
- ("r-rcistarget" ,r-rcistarget)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-aucell
+ r-data-table
+ r-dplyr
+ r-dosnow
+ r-dt
+ r-feather
+ r-fitdistrplus
+ r-genomicranges
+ r-ggplot2
+ r-lda
+ r-matrix
+ r-plyr
+ r-rcistarget
+ r-rtracklayer
+ r-s4vectors))
(home-page "https://github.com/aertslab/cisTopic")
(synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
(description
@@ -10788,24 +10566,24 @@ cisTopics and explore the nature and regulatory proteins driving them.")
"11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
(properties `((upstream-name . "cisTopic")))
(propagated-inputs
- `(("r-aucell" ,r-aucell)
- ("r-data-table" ,r-data-table)
- ("r-dosnow" ,r-dosnow)
- ("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-feather" ,r-feather)
- ("r-fitdistrplus" ,r-fitdistrplus)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-lda" ,r-lda)
- ("r-matrix" ,r-matrix)
- ("r-plyr" ,r-plyr)
- ("r-rcistarget" ,r-rcistarget)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-text2vec" ,r-text2vec)))
+ (list r-aucell
+ r-data-table
+ r-dosnow
+ r-dplyr
+ r-dt
+ r-feather
+ r-fitdistrplus
+ r-genomicranges
+ r-ggplot2
+ r-lda
+ r-matrix
+ r-plyr
+ r-rcistarget
+ r-rtracklayer
+ r-s4vectors
+ r-text2vec))
(native-inputs
- `(("r-knitr" ,r-knitr))))))
+ (list r-knitr)))))
(define-public r-genie3
(package
@@ -10821,10 +10599,9 @@ cisTopics and explore the nature and regulatory proteins driving them.")
(properties `((upstream-name . "GENIE3")))
(build-system r-build-system)
(propagated-inputs
- `(("r-dplyr" ,r-dplyr)
- ("r-reshape2" ,r-reshape2)))
+ (list r-dplyr r-reshape2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/GENIE3")
(synopsis "Gene network inference with ensemble of trees")
(description
@@ -10846,7 +10623,7 @@ regulatory networks from expression data.")
(properties `((upstream-name . "ROC")))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://www.bioconductor.org/packages/ROC/")
(synopsis "Utilities for ROC curves")
(description
@@ -10871,7 +10648,7 @@ Characteristic} (ROC) curves, with a focus on micro arrays.")
`((upstream-name
. "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
(build-system r-build-system)
- (propagated-inputs `(("r-minfi" ,r-minfi)))
+ (propagated-inputs (list r-minfi))
(home-page
"https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
(synopsis "Annotation for Illumina's 450k methylation arrays")
@@ -10894,17 +10671,16 @@ data.")
(properties `((upstream-name . "wateRmelon")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
- ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
- ("r-illuminaio" ,r-illuminaio)
- ("r-limma" ,r-limma)
- ("r-lumi" ,r-lumi)
- ("r-matrixstats" ,r-matrixstats)
- ("r-methylumi" ,r-methylumi)
- ("r-roc" ,r-roc)))
+ (list r-biobase
+ r-illuminahumanmethylation450kanno-ilmn12-hg19
+ r-illuminaio
+ r-limma
+ r-lumi
+ r-matrixstats
+ r-methylumi
+ r-roc))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/wateRmelon/")
(synopsis "Illumina 450 methylation array normalization and metrics")
(description
@@ -10955,11 +10731,9 @@ metrics, with methods for objects produced by the @code{methylumi} and
(properties `((upstream-name . "gdsfmt")))
(build-system r-build-system)
(inputs
- `(("lz4" ,lz4)
- ("xz" ,xz)
- ("zlib" ,zlib)))
+ (list lz4 xz zlib))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "http://corearray.sourceforge.net/")
(synopsis
"R Interface to CoreArray Genomic Data Structure (GDS) Files")
@@ -10991,14 +10765,14 @@ with multiple R processes supported by the package @code{parallel}.")
(properties `((upstream-name . "bigmelon")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-gdsfmt" ,r-gdsfmt)
- ("r-geoquery" ,r-geoquery)
- ("r-illuminaio" ,r-illuminaio)
- ("r-methylumi" ,r-methylumi)
- ("r-minfi" ,r-minfi)
- ("r-watermelon" ,r-watermelon)))
+ (list r-biobase
+ r-biocgenerics
+ r-gdsfmt
+ r-geoquery
+ r-illuminaio
+ r-methylumi
+ r-minfi
+ r-watermelon))
(home-page "https://bioconductor.org/packages/bigmelon/")
(synopsis "Illumina methylation array analysis for large experiments")
(description
@@ -11020,9 +10794,7 @@ with multiple R processes supported by the package @code{parallel}.")
(properties `((upstream-name . "seqbias")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rhtslib" ,r-rhtslib)))
+ (list r-biostrings r-genomicranges r-rhtslib))
(home-page "https://bioconductor.org/packages/seqbias/")
(synopsis "Estimation of per-position bias in high-throughput sequencing data")
(description
@@ -11048,13 +10820,13 @@ genome sequence.")
;; doesn't make sense to build substitutes.
(arguments `(#:substitutable? #f))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)
- ("r-iranges" ,r-iranges)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-bsgenome" ,r-bsgenome)
- ("r-biostrings" ,r-biostrings)))
+ (list r-biocgenerics
+ r-s4vectors
+ r-iranges
+ r-genomeinfodb
+ r-genomicranges
+ r-bsgenome
+ r-biostrings))
(home-page
"https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
(synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
@@ -11084,9 +10856,7 @@ injected in that sequence).")
(properties `((upstream-name . "ReQON")))
(build-system r-build-system)
(propagated-inputs
- `(("r-rjava" ,r-rjava)
- ("r-rsamtools" ,r-rsamtools)
- ("r-seqbias" ,r-seqbias)))
+ (list r-rjava r-rsamtools r-seqbias))
(home-page "https://bioconductor.org/packages/ReQON/")
(synopsis "Recalibrating quality of nucleotides")
(description
@@ -11109,22 +10879,22 @@ format.")
(properties `((upstream-name . "wavClusteR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-foreach" ,r-foreach)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-mclust" ,r-mclust)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqinr" ,r-seqinr)
- ("r-stringr" ,r-stringr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-foreach
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-hmisc
+ r-iranges
+ r-mclust
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-seqinr
+ r-stringr))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/wavClusteR/")
(synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
(description
@@ -11157,23 +10927,23 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
`((upstream-name . "TimeSeriesExperiment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-deseq2" ,r-deseq2)
- ("r-dplyr" ,r-dplyr)
- ("r-dynamictreecut" ,r-dynamictreecut)
- ("r-edger" ,r-edger)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hmisc" ,r-hmisc)
- ("r-limma" ,r-limma)
- ("r-magrittr" ,r-magrittr)
- ("r-proxy" ,r-proxy)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-vegan" ,r-vegan)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-deseq2
+ r-dplyr
+ r-dynamictreecut
+ r-edger
+ r-ggplot2
+ r-hmisc
+ r-limma
+ r-magrittr
+ r-proxy
+ r-s4vectors
+ r-summarizedexperiment
+ r-tibble
+ r-tidyr
+ r-vegan
+ r-viridis))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
(synopsis "Analysis for short time-series data")
(description
@@ -11198,30 +10968,30 @@ provides methods for retrieving enriched pathways.")
`((upstream-name . "VariantFiltering")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-dt" ,r-dt)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-genomicscores" ,r-genomicscores)
- ("r-graph" ,r-graph)
- ("r-gviz" ,r-gviz)
- ("r-iranges" ,r-iranges)
- ("r-rbgl" ,r-rbgl)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-shinyjs" ,r-shinyjs)
- ("r-shinythemes" ,r-shinythemes)
- ("r-shinytree" ,r-shinytree)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)
- ("r-xvector" ,r-xvector)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-dt
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-genomicscores
+ r-graph
+ r-gviz
+ r-iranges
+ r-rbgl
+ r-rsamtools
+ r-s4vectors
+ r-shiny
+ r-shinyjs
+ r-shinythemes
+ r-shinytree
+ r-summarizedexperiment
+ r-variantannotation
+ r-xvector))
(home-page "https://github.com/rcastelo/VariantFiltering")
(synopsis "Filtering of coding and non-coding genetic variants")
(description
@@ -11244,7 +11014,7 @@ populations, splice site strength, conservation, etc.")
(properties `((upstream-name . "GenomeGraphs")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biomart" ,r-biomart)))
+ (list r-biomart))
(home-page "https://bioconductor.org/packages/GenomeGraphs/")
(synopsis "Plotting genomic information from Ensembl")
(description
@@ -11272,16 +11042,16 @@ same genome coordinate system.")
(properties `((upstream-name . "waveTiling")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-genomegraphs" ,r-genomegraphs)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-oligo" ,r-oligo)
- ("r-oligoclasses" ,r-oligoclasses)
- ("r-preprocesscore" ,r-preprocesscore)
- ("r-waveslim" ,r-waveslim)))
+ (list r-affy
+ r-biobase
+ r-biostrings
+ r-genomegraphs
+ r-genomicranges
+ r-iranges
+ r-oligo
+ r-oligoclasses
+ r-preprocesscore
+ r-waveslim))
(home-page "https://r-forge.r-project.org/projects/wavetiling/")
(synopsis "Wavelet-based models for tiling array transcriptome analysis")
(description
@@ -11304,25 +11074,25 @@ arrays based on fast wavelet-based functional models.")
`((upstream-name . "variancePartition")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocparallel" ,r-biocparallel)
- ("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gplots" ,r-gplots)
- ("r-iterators" ,r-iterators)
- ("r-limma" ,r-limma)
- ("r-lme4" ,r-lme4)
- ("r-lmertest" ,r-lmertest)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-pbkrtest" ,r-pbkrtest)
- ("r-progress" ,r-progress)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-scales" ,r-scales)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocparallel
+ r-doparallel
+ r-foreach
+ r-ggplot2
+ r-gplots
+ r-iterators
+ r-limma
+ r-lme4
+ r-lmertest
+ r-mass
+ r-matrix
+ r-pbkrtest
+ r-progress
+ r-reshape2
+ r-rlang
+ r-scales))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/variancePartition/")
(synopsis "Analyze variation in gene expression experiments")
(description
@@ -11348,11 +11118,7 @@ measures.")
(properties `((upstream-name . "HTqPCR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-gplots" ,r-gplots)
- ("r-limma" ,r-limma)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
(home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
"groups/bertone/software/HTqPCR.pdf"))
(synopsis "Automated analysis of high-throughput qPCR data")
@@ -11383,8 +11149,7 @@ features (e.g. genes, microRNAs).")
`((upstream-name . "unifiedWMWqPCR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-htqpcr" ,r-htqpcr)))
+ (list r-biocgenerics r-htqpcr))
(home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
(synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
(description
@@ -11415,18 +11180,18 @@ data.")
(substitute* "src/Makevars"
(("/usr/bin/strip") (which "strip"))))))))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-mass" ,r-mass)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppthread" ,r-rcppthread)
- ("r-rlang" ,r-rlang)
- ("r-s4vectors" ,r-s4vectors)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biostrings
+ r-ggplot2
+ r-iranges
+ r-mass
+ r-rcpp
+ r-rcppthread
+ r-rlang
+ r-s4vectors
+ r-yaml))
+ (native-inputs
+ (list r-knitr))
(home-page
"https://bioconductor.org/packages/universalmotif/")
(synopsis
@@ -11458,15 +11223,15 @@ motifs, and others.")
`((upstream-name . "ActiveDriverWGS")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biostrings
+ r-bsgenome
+ r-bsgenome-hsapiens-ucsc-hg19
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
(synopsis "Driver discovery tool for cancer whole genomes")
(description
@@ -11493,10 +11258,9 @@ using whole genome sequencing data.")
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-ggplot2" ,r-ggplot2)))
+ (list r-data-table r-ggplot2))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://cran.r-project.org/web/packages/ActivePathways/")
(synopsis "Multivariate pathway enrichment analysis")
(description
@@ -11521,7 +11285,7 @@ cellular organization in health and disease.")
(properties `((upstream-name . "BGmix")))
(build-system r-build-system)
(propagated-inputs
- `(("r-kernsmooth" ,r-kernsmooth)))
+ (list r-kernsmooth))
(home-page "https://bioconductor.org/packages/BGmix/")
(synopsis "Bayesian models for differential gene expression")
(description
@@ -11543,10 +11307,7 @@ gene expression.")
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
(propagated-inputs
- `(("r-affy" ,r-affy)
- ("r-biobase" ,r-biobase)
- ("r-gcrma" ,r-gcrma)
- ("r-rcpp" ,r-rcpp)))
+ (list r-affy r-biobase r-gcrma r-rcpp))
(home-page "https://bioconductor.org/packages/bgx/")
(synopsis "Bayesian gene expression")
(description
@@ -11594,9 +11355,7 @@ algorithm which is more efficient for larger data sets.")
(properties `((upstream-name . "BicARE")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-gseabase" ,r-gseabase)
- ("r-multtest" ,r-multtest)))
+ (list r-biobase r-gseabase r-multtest))
(home-page "http://bioinfo.curie.fr")
(synopsis "Biclustering analysis and results exploration")
(description
@@ -11618,10 +11377,9 @@ results.")
(properties `((upstream-name . "BiFET")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-poibin" ,r-poibin)))
+ (list r-genomicranges r-poibin))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiFET")
(synopsis "Bias-free footprint enrichment test")
(description
@@ -11648,12 +11406,11 @@ the read count and GC content bias.")
(properties `((upstream-name . "rsbml")))
(build-system r-build-system)
(inputs
- `(("libsbml" ,libsbml)))
+ (list libsbml))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-graph" ,r-graph)))
+ (list r-biocgenerics r-graph))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "http://www.sbml.org")
(synopsis "R support for SBML")
(description
@@ -11675,7 +11432,7 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
(properties `((upstream-name . "hypergraph")))
(build-system r-build-system)
(propagated-inputs
- `(("r-graph" ,r-graph)))
+ (list r-graph))
(home-page "https://bioconductor.org/packages/hypergraph")
(synopsis "Hypergraph data structures")
(description
@@ -11696,11 +11453,9 @@ manipulating hypergraphs.")
"1lkiqrk01hshms9ghsfynxwj69zr3463r3rg8rn7hkwn3bj8xyzj"))))
(properties `((upstream-name . "hyperdraw")))
(build-system r-build-system)
- (inputs `(("graphviz" ,graphviz)))
+ (inputs (list graphviz))
(propagated-inputs
- `(("r-graph" ,r-graph)
- ("r-hypergraph" ,r-hypergraph)
- ("r-rgraphviz" ,r-rgraphviz)))
+ (list r-graph r-hypergraph r-rgraphviz))
(home-page "https://bioconductor.org/packages/hyperdraw")
(synopsis "Visualizing hypergraphs")
(description
@@ -11721,12 +11476,12 @@ manipulating hypergraphs.")
(properties `((upstream-name . "BiGGR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-hyperdraw" ,r-hyperdraw)
- ("r-hypergraph" ,r-hypergraph)
- ("r-lim" ,r-lim)
- ("r-limsolve" ,r-limsolve)
- ("r-rsbml" ,r-rsbml)
- ("r-stringr" ,r-stringr)))
+ (list r-hyperdraw
+ r-hypergraph
+ r-lim
+ r-limsolve
+ r-rsbml
+ r-stringr))
(home-page "https://bioconductor.org/packages/BiGGR/")
(synopsis "Constraint based modeling using metabolic reconstruction databases")
(description
@@ -11752,9 +11507,9 @@ networks and estimated fluxes can be visualized with hypergraphs.")
`((upstream-name . "bigmemoryExtras")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bigmemory" ,r-bigmemory)))
+ (list r-bigmemory))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/phaverty/bigmemoryExtras")
(synopsis "Extension of the bigmemory package")
(description
@@ -11785,26 +11540,26 @@ a file-backed matrix with factor properties.")
(properties `((upstream-name . "bigPint")))
(build-system r-build-system)
(propagated-inputs
- `(("r-delayedarray" ,r-delayedarray)
- ("r-dplyr" ,r-dplyr)
- ("r-ggally" ,r-ggally)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-hexbin" ,r-hexbin)
- ("r-hmisc" ,r-hmisc)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-plotly" ,r-plotly)
- ("r-plyr" ,r-plyr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape" ,r-reshape)
- ("r-shiny" ,r-shiny)
- ("r-shinycssloaders" ,r-shinycssloaders)
- ("r-shinydashboard" ,r-shinydashboard)
- ("r-stringr" ,r-stringr)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tidyr" ,r-tidyr)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-delayedarray
+ r-dplyr
+ r-ggally
+ r-ggplot2
+ r-gridextra
+ r-hexbin
+ r-hmisc
+ r-htmlwidgets
+ r-plotly
+ r-plyr
+ r-rcolorbrewer
+ r-reshape
+ r-shiny
+ r-shinycssloaders
+ r-shinydashboard
+ r-stringr
+ r-summarizedexperiment
+ r-tidyr))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/lindsayrutter/bigPint")
(synopsis "Big multivariate data plotted interactively")
(description
@@ -11828,23 +11583,23 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
(properties `((upstream-name . "ChemmineR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-base64enc" ,r-base64enc)
- ("r-bh" ,r-bh)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-digest" ,r-digest)
- ("r-dt" ,r-dt)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-jsonlite" ,r-jsonlite)
- ("r-png" ,r-png)
- ("r-rcpp" ,r-rcpp)
- ("r-rcurl" ,r-rcurl)
- ("r-rjson" ,r-rjson)
- ("r-rsvg" ,r-rsvg)
- ("r-stringi" ,r-stringi)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-base64enc
+ r-bh
+ r-biocgenerics
+ r-dbi
+ r-digest
+ r-dt
+ r-ggplot2
+ r-gridextra
+ r-jsonlite
+ r-png
+ r-rcpp
+ r-rcurl
+ r-rjson
+ r-rsvg
+ r-stringi))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/girke-lab/ChemmineR")
(synopsis "Cheminformatics toolkit for R")
(description
@@ -11870,10 +11625,8 @@ structures.")
(properties `((upstream-name . "fmcsR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-chemminer" ,r-chemminer)
- ("r-runit" ,r-runit)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics r-chemminer r-runit))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/girke-lab/fmcsR")
(synopsis "Mismatch tolerant maximum common substructure searching")
(description
@@ -11902,15 +11655,15 @@ searching and clustering.")
(properties `((upstream-name . "bioassayR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-chemminer" ,r-chemminer)
- ("r-dbi" ,r-dbi)
- ("r-matrix" ,r-matrix)
- ("r-rjson" ,r-rjson)
- ("r-rsqlite" ,r-rsqlite)
- ("r-xml" ,r-xml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-chemminer
+ r-dbi
+ r-matrix
+ r-rjson
+ r-rsqlite
+ r-xml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/girke-lab/bioassayR")
(synopsis "Cross-target analysis of small molecule bioactivity")
(description
@@ -11937,12 +11690,9 @@ available bioactivity data.")
(properties `((upstream-name . "biobroom")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-broom" ,r-broom)
- ("r-dplyr" ,r-dplyr)
- ("r-tidyr" ,r-tidyr)))
+ (list r-biobase r-broom r-dplyr r-tidyr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/StoreyLab/biobroom")
(synopsis "Turn Bioconductor objects into tidy data frames")
(description
@@ -11969,11 +11719,7 @@ visualize bioinformatics analyses.")
(properties `((upstream-name . "graphite")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-checkmate" ,r-checkmate)
- ("r-graph" ,r-graph)
- ("r-httr" ,r-httr)
- ("r-rappdirs" ,r-rappdirs)))
+ (list r-annotationdbi r-checkmate r-graph r-httr r-rappdirs))
(home-page "https://bioconductor.org/packages/graphite/")
(synopsis "Networks from pathway databases")
(description
@@ -11996,16 +11742,16 @@ symbols).")
(properties `((upstream-name . "ReactomePA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dose" ,r-dose)
- ("r-enrichplot" ,r-enrichplot)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggraph" ,r-ggraph)
- ("r-graphite" ,r-graphite)
- ("r-igraph" ,r-igraph)
- ("r-reactome-db" ,r-reactome-db)))
+ (list r-annotationdbi
+ r-dose
+ r-enrichplot
+ r-ggplot2
+ r-ggraph
+ r-graphite
+ r-igraph
+ r-reactome-db))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://guangchuangyu.github.io/software/ReactomePA")
(synopsis "Reactome pathway analysis")
(description
@@ -12028,9 +11774,7 @@ enrichment analysis and several functions for visualization.")
(properties `((upstream-name . "EBarrays")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-cluster" ,r-cluster)
- ("r-lattice" ,r-lattice)))
+ (list r-biobase r-cluster r-lattice))
(home-page "https://bioconductor.org/packages/EBarrays/")
(synopsis "Gene clustering and differential expression identification")
(description
@@ -12052,7 +11796,7 @@ microarray data.")
(properties
`((upstream-name . "BiocCaseStudies")))
(build-system r-build-system)
- (propagated-inputs `(("r-biobase" ,r-biobase)))
+ (propagated-inputs (list r-biobase))
(home-page "https://bioconductor.org/packages/BiocCaseStudies")
(synopsis "Support for the case studies monograph")
(description
@@ -12074,16 +11818,16 @@ monograph.")
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(propagated-inputs
- `(("r-codetools" ,r-codetools)
- ("r-graph" ,r-graph)
- ("r-httr" ,r-httr)
- ("r-knitr" ,r-knitr)
- ("r-optparse" ,r-optparse)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biocviews" ,r-biocviews)
- ("r-stringdist" ,r-stringdist)))
+ (list r-codetools
+ r-graph
+ r-httr
+ r-knitr
+ r-optparse
+ r-biocmanager
+ r-biocviews
+ r-stringdist))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocCheck")
(synopsis "Executes Bioconductor-specific package checks")
(description "This package contains tools to perform additional quality
@@ -12104,10 +11848,7 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(properties `((upstream-name . "biocGraph")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-geneplotter" ,r-geneplotter)
- ("r-graph" ,r-graph)
- ("r-rgraphviz" ,r-rgraphviz)))
+ (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
(home-page "https://bioconductor.org/packages/biocGraph/")
(synopsis "Graph examples and use cases in Bioinformatics")
(description
@@ -12129,13 +11870,9 @@ different graph related packages produced by Bioconductor.")
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocmanager" ,r-biocmanager)
- ("r-bookdown" ,r-bookdown)
- ("r-knitr" ,r-knitr)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-yaml" ,r-yaml)))
+ (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocStyle")
(synopsis "Bioconductor formatting styles")
(description "This package provides standard formatting styles for
@@ -12157,13 +11894,13 @@ functionality.")
`((upstream-name . "biocViews")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocmanager" ,r-biocmanager)
- ("r-graph" ,r-graph)
- ("r-rbgl" ,r-rbgl)
- ("r-rcurl" ,r-rcurl)
- ("r-xml" ,r-xml)
- ("r-runit" ,r-runit)))
+ (list r-biobase
+ r-biocmanager
+ r-graph
+ r-rbgl
+ r-rcurl
+ r-xml
+ r-runit))
(home-page "https://bioconductor.org/packages/biocViews")
(synopsis "Bioconductor package categorization helper")
(description "The purpose of biocViews is to create HTML pages that
@@ -12185,15 +11922,15 @@ also known as views, in a controlled vocabulary.")
(properties `((upstream-name . "ExperimentHub")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocmanager" ,r-biocmanager)
- ("r-curl" ,r-curl)
- ("r-rappdirs" ,r-rappdirs)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-annotationhub
+ r-biocfilecache
+ r-biocgenerics
+ r-biocmanager
+ r-curl
+ r-rappdirs
+ r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ExperimentHub/")
(synopsis "Client to access ExperimentHub resources")
(description
@@ -12219,13 +11956,13 @@ access.")
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-mass" ,r-mass)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-mass
+ r-rtracklayer
+ r-s4vectors))
(home-page "https://github.com/Kraus-Lab/groHMM")
(synopsis "GRO-seq analysis pipeline")
(description
@@ -12247,15 +11984,15 @@ access.")
`((upstream-name . "MultiAssayExperiment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tidyr" ,r-tidyr)))
+ (list r-biobase
+ r-biocgenerics
+ r-genomicranges
+ r-iranges
+ r-s4vectors
+ r-summarizedexperiment
+ r-tidyr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://waldronlab.io/MultiAssayExperiment/")
(synopsis "Integration of multi-omics experiments in Bioconductor")
(description
@@ -12281,30 +12018,30 @@ rownames.")
(properties `((upstream-name . "BiocOncoTK")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bigrquery" ,r-bigrquery)
- ("r-car" ,r-car)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-curatedtcgadata" ,r-curatedtcgadata)
- ("r-dbi" ,r-dbi)
- ("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggpubr" ,r-ggpubr)
- ("r-graph" ,r-graph)
- ("r-httr" ,r-httr)
- ("r-iranges" ,r-iranges)
- ("r-magrittr" ,r-magrittr)
- ("r-plyr" ,r-plyr)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rjson" ,r-rjson)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-bigrquery
+ r-car
+ r-complexheatmap
+ r-curatedtcgadata
+ r-dbi
+ r-dplyr
+ r-dt
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-ggpubr
+ r-graph
+ r-httr
+ r-iranges
+ r-magrittr
+ r-plyr
+ r-rgraphviz
+ r-rjson
+ r-s4vectors
+ r-scales
+ r-shiny
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocOncoTK")
(synopsis "Bioconductor components for general cancer genomics")
(description
@@ -12326,11 +12063,9 @@ tools for genome-scale analysis of cancer studies.")
(properties `((upstream-name . "BioCor")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-gseabase" ,r-gseabase)
- ("r-matrix" ,r-matrix)))
+ (list r-biocparallel r-gseabase r-matrix))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://llrs.github.io/BioCor/")
(synopsis "Functional similarities")
(description
@@ -12355,30 +12090,30 @@ gene selection, testing relationships, and so on.")
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocfilecache" ,r-biocfilecache)
- ("r-biocmanager" ,r-biocmanager)
- ("r-biocviews" ,r-biocviews)
- ("r-dplyr" ,r-dplyr)
- ("r-dt" ,r-dt)
- ("r-gh" ,r-gh)
- ("r-graph" ,r-graph)
- ("r-htmltools" ,r-htmltools)
- ("r-htmlwidgets" ,r-htmlwidgets)
- ("r-httr" ,r-httr)
- ("r-igraph" ,r-igraph)
- ("r-jsonlite" ,r-jsonlite)
- ("r-magrittr" ,r-magrittr)
- ("r-rbgl" ,r-rbgl)
- ("r-readr" ,r-readr)
- ("r-rlang" ,r-rlang)
- ("r-rvest" ,r-rvest)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-tidyselect" ,r-tidyselect)
- ("r-xml2" ,r-xml2)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocfilecache
+ r-biocmanager
+ r-biocviews
+ r-dplyr
+ r-dt
+ r-gh
+ r-graph
+ r-htmltools
+ r-htmlwidgets
+ r-httr
+ r-igraph
+ r-jsonlite
+ r-magrittr
+ r-rbgl
+ r-readr
+ r-rlang
+ r-rvest
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect
+ r-xml2))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/seandavi/BiocPkgTools")
(synopsis "Collection of tools for learning about Bioconductor packages")
(description
@@ -12403,18 +12138,18 @@ analytics on packages.")
(properties `((upstream-name . "BiocSet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biocio" ,r-biocio)
- ("r-dplyr" ,r-dplyr)
- ("r-keggrest" ,r-keggrest)
- ("r-ontologyindex" ,r-ontologyindex)
- ("r-plyr" ,r-plyr)
- ("r-rlang" ,r-rlang)
- ("r-s4vectors" ,r-s4vectors)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)))
+ (list r-annotationdbi
+ r-biocio
+ r-dplyr
+ r-keggrest
+ r-ontologyindex
+ r-plyr
+ r-rlang
+ r-s4vectors
+ r-tibble
+ r-tidyr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page
"https://bioconductor.org/packages/BiocSet")
(synopsis
@@ -12442,17 +12177,17 @@ accessing web references for elements/sets are also available in BiocSet.")
`((upstream-name . "BiocWorkflowTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocstyle" ,r-biocstyle)
- ("r-bookdown" ,r-bookdown)
- ("r-git2r" ,r-git2r)
- ("r-httr" ,r-httr)
- ("r-knitr" ,r-knitr)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-rstudioapi" ,r-rstudioapi)
- ("r-stringr" ,r-stringr)
- ("r-usethis" ,r-usethis)))
+ (list r-biocstyle
+ r-bookdown
+ r-git2r
+ r-httr
+ r-knitr
+ r-rmarkdown
+ r-rstudioapi
+ r-stringr
+ r-usethis))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
(synopsis "Tools to aid the development of Bioconductor Workflow packages")
(description
@@ -12474,8 +12209,7 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
(properties `((upstream-name . "bioDist")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-kernsmooth" ,r-kernsmooth)))
+ (list r-biobase r-kernsmooth))
(home-page "https://bioconductor.org/packages/bioDist/")
(synopsis "Different distance measures")
(description
@@ -12497,21 +12231,21 @@ distance measures.")
(properties `((upstream-name . "PCAtools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-bh" ,r-bh)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-cowplot" ,r-cowplot)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dqrng" ,r-dqrng)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-lattice" ,r-lattice)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-reshape2" ,r-reshape2)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-bh
+ r-biocparallel
+ r-biocsingular
+ r-cowplot
+ r-delayedarray
+ r-delayedmatrixstats
+ r-dqrng
+ r-ggplot2
+ r-ggrepel
+ r-lattice
+ r-matrix
+ r-rcpp
+ r-reshape2))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/kevinblighe/PCAtools")
(synopsis "PCAtools: everything Principal Components Analysis")
(description
@@ -12543,12 +12277,8 @@ dimensional mass cytometry data.")
(properties `((upstream-name . "rGREAT")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-getoptlong" ,r-getoptlong)
- ("r-iranges" ,r-iranges)
- ("r-rcurl" ,r-rcurl)
- ("r-rjson" ,r-rjson)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/jokergoo/rGREAT")
(synopsis "Client for GREAT analysis")
(description
@@ -12571,17 +12301,17 @@ user's input and automatically retrieving results from GREAT web server.")
(properties `((upstream-name . "M3C")))
(build-system r-build-system)
(propagated-inputs
- `(("r-cluster" ,r-cluster)
- ("r-corpcor" ,r-corpcor)
- ("r-doparallel" ,r-doparallel)
- ("r-dosnow" ,r-dosnow)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-matrix" ,r-matrix)
- ("r-matrixcalc" ,r-matrixcalc)
- ("r-rtsne" ,r-rtsne)
- ("r-umap" ,r-umap)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-cluster
+ r-corpcor
+ r-doparallel
+ r-dosnow
+ r-foreach
+ r-ggplot2
+ r-matrix
+ r-matrixcalc
+ r-rtsne
+ r-umap))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/M3C")
(synopsis "Monte Carlo reference-based consensus clustering")
(description
@@ -12604,7 +12334,7 @@ hypothesis @code{K=1}.")
(properties `((upstream-name . "Icens")))
(build-system r-build-system)
(propagated-inputs
- `(("r-survival" ,r-survival)))
+ (list r-survival))
(home-page "https://bioconductor.org/packages/Icens")
(synopsis "NPMLE for censored and truncated data")
(description
@@ -12629,10 +12359,7 @@ truncated data.")
(properties `((upstream-name . "interval")))
(build-system r-build-system)
(propagated-inputs
- `(("r-icens" ,r-icens)
- ("r-mlecens" ,r-mlecens)
- ("r-perm" ,r-perm)
- ("r-survival" ,r-survival)))
+ (list r-icens r-mlecens r-perm r-survival))
(home-page "https://cran.r-project.org/web/packages/interval/")
(synopsis "Weighted Logrank tests and NPMLE for interval censored data")
(description
@@ -12656,11 +12383,7 @@ plot them, and perform logrank or Wilcoxon type tests.")
(properties `((upstream-name . "FHtest")))
(build-system r-build-system)
(propagated-inputs
- `(("r-interval" ,r-interval)
- ("r-kmsurv" ,r-kmsurv)
- ("r-mass" ,r-mass)
- ("r-perm" ,r-perm)
- ("r-survival" ,r-survival)))
+ (list r-interval r-kmsurv r-mass r-perm r-survival))
(home-page "https://cran.r-project.org/web/packages/FHtest/")
(synopsis "Tests for survival data based on the Fleming-Harrington class")
(description
@@ -12689,23 +12412,23 @@ with:
(properties `((upstream-name . "FourCSeq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biostrings" ,r-biostrings)
- ("r-deseq2" ,r-deseq2)
- ("r-fda" ,r-fda)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbio" ,r-ggbio)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gtools" ,r-gtools)
- ("r-lsd" ,r-lsd)
- ("r-matrix" ,r-matrix)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biostrings
+ r-deseq2
+ r-fda
+ r-genomicalignments
+ r-genomicranges
+ r-ggbio
+ r-ggplot2
+ r-gtools
+ r-lsd
+ r-matrix
+ r-reshape2
+ r-rsamtools
+ r-rtracklayer
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page
"https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
(synopsis "Analysis of multiplexed 4C sequencing data")
@@ -12755,7 +12478,7 @@ routines.")
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)))
+ (list r-biocgenerics))
(home-page "https://bioconductor.org/packages/S4Vectors")
(synopsis "S4 implementation of vectors and lists")
(description
@@ -12784,18 +12507,18 @@ S4Vectors package itself.")
(properties `((upstream-name . "WGCNA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-doparallel" ,r-doparallel)
- ("r-dynamictreecut" ,r-dynamictreecut)
- ("r-fastcluster" ,r-fastcluster)
- ("r-foreach" ,r-foreach)
- ("r-go-db" ,r-go-db)
- ("r-hmisc" ,r-hmisc)
- ("r-impute" ,r-impute)
- ("r-rcpp" ,r-rcpp)
- ("r-survival" ,r-survival)
- ("r-matrixstats" ,r-matrixstats)
- ("r-preprocesscore" ,r-preprocesscore)))
+ (list r-annotationdbi
+ r-doparallel
+ r-dynamictreecut
+ r-fastcluster
+ r-foreach
+ r-go-db
+ r-hmisc
+ r-impute
+ r-rcpp
+ r-survival
+ r-matrixstats
+ r-preprocesscore))
(home-page
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
(synopsis "Weighted correlation network analysis")
@@ -12834,11 +12557,11 @@ data manipulation and visualization.")
;; FIXME: Rgraphviz bundles the sources of an older variant of
;; graphviz. It does not build with the latest version of graphviz, so
;; we do not add graphviz to the inputs.
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(propagated-inputs
- `(("r-graph" ,r-graph)))
+ (list r-graph))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://bioconductor.org/packages/Rgraphviz")
(synopsis "Plotting capabilities for R graph objects")
(description
@@ -12859,11 +12582,9 @@ objects from the @code{graph} package.")
(properties `((upstream-name . "FitHiC")))
(build-system r-build-system)
(propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-fdrtool" ,r-fdrtool)
- ("r-rcpp" ,r-rcpp)))
+ (list r-data-table r-fdrtool r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/FitHiC")
(synopsis "Confidence estimation for intra-chromosomal contact maps")
(description
@@ -12885,13 +12606,13 @@ assays such as Hi-C.")
(properties `((upstream-name . "HiTC")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)))
+ (list r-biostrings
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rcolorbrewer
+ r-rtracklayer))
(home-page "https://bioconductor.org/packages/HiTC")
(synopsis "High throughput chromosome conformation capture analysis")
(description
@@ -12915,16 +12636,16 @@ provided.")
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rhdf5filters" ,r-rhdf5filters)
- ("r-rhdf5lib" ,r-rhdf5lib)
- ("r-s4vectors" ,r-s4vectors)))
+ (list zlib))
+ (propagated-inputs
+ (list r-biocgenerics
+ r-delayedarray
+ r-iranges
+ r-matrix
+ r-rhdf5
+ r-rhdf5filters
+ r-rhdf5lib
+ r-s4vectors))
(home-page "https://bioconductor.org/packages/HDF5Array")
(synopsis "HDF5 back end for DelayedArray objects")
(description "This package provides an array-like container for convenient
@@ -13004,8 +12725,7 @@ block processing.")
(("cp \"\\$\\{SZIP_LIB\\}.*") "")
(("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
(propagated-inputs
- `(("hdf5" ,hdf5-1.10)
- ("zlib" ,zlib)))
+ (list hdf5-1.10 zlib))
(native-inputs
`(("hdf5-source" ,(package-source hdf5-1.10))
("r-knitr" ,r-knitr)))
@@ -13028,12 +12748,9 @@ packages.")
"1l8c9q35mf90ckb366bcfqa0v2gw7ahs2h362j7cwv8fp39h4mpb"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)))
+ (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/beachmat")
(synopsis "Compiling Bioconductor to handle each matrix type")
(description "This package provides a consistent C++ class interface for a
@@ -13056,29 +12773,29 @@ matrices.")
(base32 "0w4iqmyyhsb6l9bi8c6qwdh4j6z2i1i5fi85ia9069fpl9d0hpl2"))))
(properties `((upstream-name . "CNEr")))
(build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
- (propagated-inputs
- `(("r-annotate" ,r-annotate)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-dbi" ,r-dbi)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-go-db" ,r-go-db)
- ("r-iranges" ,r-iranges)
- ("r-keggrest" ,r-keggrest)
- ("r-powerlaw" ,r-powerlaw)
- ("r-r-utils" ,r-r-utils)
- ("r-readr" ,r-readr)
- ("r-reshape2" ,r-reshape2)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (inputs (list zlib))
+ (propagated-inputs
+ (list r-annotate
+ r-biocgenerics
+ r-biostrings
+ r-dbi
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-go-db
+ r-iranges
+ r-keggrest
+ r-powerlaw
+ r-r-utils
+ r-readr
+ r-reshape2
+ r-rsqlite
+ r-rtracklayer
+ r-s4vectors
+ r-xvector))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/ge11232002/CNEr")
(synopsis "CNE Detection and Visualization")
(description
@@ -13106,27 +12823,27 @@ advanced visualization of sets of conserved noncoding elements.")
(properties `((upstream-name . "TFBSTools")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-catools" ,r-catools)
- ("r-cner" ,r-cner)
- ("r-dbi" ,r-dbi)
- ("r-dirichletmultinomial" ,r-dirichletmultinomial)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-iranges" ,r-iranges)
- ("r-rsqlite" ,r-rsqlite)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-seqlogo" ,r-seqlogo)
- ("r-tfmpvalue" ,r-tfmpvalue)
- ("r-xml" ,r-xml)
- ("r-xvector" ,r-xvector)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-catools
+ r-cner
+ r-dbi
+ r-dirichletmultinomial
+ r-genomeinfodb
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-rsqlite
+ r-rtracklayer
+ r-s4vectors
+ r-seqlogo
+ r-tfmpvalue
+ r-xml
+ r-xvector))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/ge11232002/TFBSTools")
(synopsis "Transcription factor binding site (TFBS) analysis")
(description
@@ -13152,19 +12869,19 @@ provides a wrapper of de novo motif discovery software.")
(properties `((upstream-name . "motifmatchr")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tfbstools" ,r-tfbstools)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biostrings
+ r-bsgenome
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rcpp
+ r-rcpparmadillo
+ r-rsamtools
+ r-s4vectors
+ r-summarizedexperiment
+ r-tfbstools))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/motifmatchr")
(synopsis "Fast motif matching in R")
(description
@@ -13185,29 +12902,29 @@ This package wraps C++ code from the MOODS motif calling library.")
(properties `((upstream-name . "chromVAR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-dt" ,r-dt)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-miniui" ,r-miniui)
- ("r-nabor" ,r-nabor)
- ("r-plotly" ,r-plotly)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtsne" ,r-rtsne)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tfbstools" ,r-tfbstools)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-dt
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-matrix
+ r-miniui
+ r-nabor
+ r-plotly
+ r-rcolorbrewer
+ r-rcpp
+ r-rcpparmadillo
+ r-rsamtools
+ r-rtsne
+ r-s4vectors
+ r-shiny
+ r-summarizedexperiment
+ r-tfbstools))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
(synopsis "Determine chromatin variation across regions")
(description
@@ -13234,13 +12951,10 @@ sequence (@code{DNAse-seq}) experiments.")
`((upstream-name . "SingleCellExperiment")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-genomicranges" ,r-genomicranges)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
+ r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/SingleCellExperiment")
(synopsis "S4 classes for single cell data")
(description "This package defines an S4 class for storing data from
@@ -13264,18 +12978,18 @@ libraries.")
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-genomicranges" ,r-genomicranges)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-biocgenerics
+ r-biocparallel
+ r-delayedarray
+ r-delayedmatrixstats
+ r-genomicranges
+ r-matrix
+ r-rcpp
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/scuttle")
(synopsis "Single-cell RNA-Seq analysis utilities")
(description
@@ -13297,28 +13011,28 @@ of other packages.")
"0k4i9pwmwxcr5a40ljl27wriccwn5vc52xy48yjjh8ppl5dbggdg"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-gridextra" ,r-gridextra)
- ("r-matrix" ,r-matrix)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rlang" ,r-rlang)
- ("r-rtsne" ,r-rtsne)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scuttle" ,r-scuttle)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-biocgenerics
+ r-biocneighbors
+ r-biocparallel
+ r-biocsingular
+ r-delayedarray
+ r-delayedmatrixstats
+ r-ggbeeswarm
+ r-ggplot2
+ r-ggrepel
+ r-gridextra
+ r-matrix
+ r-rcolorbrewer
+ r-rlang
+ r-rtsne
+ r-s4vectors
+ r-scuttle
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-viridis))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/davismcc/scater")
(synopsis "Single-cell analysis toolkit for gene expression data in R")
(description "This package provides a collection of tools for doing
@@ -13339,28 +13053,28 @@ quality control.")
"06lcxya6rpa8dv0il7m7fwyx0ci1y1jn16ff5lmvzf2mnr6q7lic"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-bh" ,r-bh)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-bluster" ,r-bluster)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dqrng" ,r-dqrng)
- ("r-edger" ,r-edger)
- ("r-igraph" ,r-igraph)
- ("r-limma" ,r-limma)
- ("r-matrix" ,r-matrix)
- ("r-metapod" ,r-metapod)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scuttle" ,r-scuttle)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-statmod" ,r-statmod)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-bh
+ r-biocgenerics
+ r-biocparallel
+ r-biocsingular
+ r-bluster
+ r-delayedarray
+ r-delayedmatrixstats
+ r-dqrng
+ r-edger
+ r-igraph
+ r-limma
+ r-matrix
+ r-metapod
+ r-rcpp
+ r-s4vectors
+ r-scuttle
+ r-singlecellexperiment
+ r-statmod
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/scran")
(synopsis "Methods for single-cell RNA-Seq data analysis")
(description "This package implements a variety of low-level analyses of
@@ -13384,11 +13098,8 @@ variable and significantly correlated genes.")
`((upstream-name . "sparseMatrixStats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-matrix" ,r-matrix)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rcpp" ,r-rcpp)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/sparseMatrixStats/")
(synopsis "Summary statistics for rows and columns of sparse matrices")
(description
@@ -13412,15 +13123,15 @@ data in the column sparse format.")
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-delayedarray" ,r-delayedarray)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-matrixgenerics" ,r-matrixgenerics)
- ("r-matrixstats" ,r-matrixstats)
- ("r-s4vectors" ,r-s4vectors)
- ("r-sparsematrixstats" ,r-sparsematrixstats)))
+ (list r-delayedarray
+ r-iranges
+ r-matrix
+ r-matrixgenerics
+ r-matrixstats
+ r-s4vectors
+ r-sparsematrixstats))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
(synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
(description
@@ -13447,12 +13158,9 @@ memory usage and processing time is minimized.")
(properties `((upstream-name . "MsCoreUtils")))
(build-system r-build-system)
(propagated-inputs
- `(("r-clue" ,r-clue)
- ("r-mass" ,r-mass)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-clue r-mass r-rcpp r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
(synopsis "Core utils for mass spectrometry data")
(description
@@ -13478,11 +13186,9 @@ within the R for Mass Spectrometry packages.")
(properties `((upstream-name . "MsFeatures")))
(build-system r-build-system)
(propagated-inputs
- `(("r-mscoreutils" ,r-mscoreutils)
- ("r-protgenerics" ,r-protgenerics)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (list r-mscoreutils r-protgenerics r-summarizedexperiment))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/RforMassSpectrometry/MsFeatures")
(synopsis "Functionality for mass spectrometry features")
(description
@@ -13511,10 +13217,9 @@ the respective packages (such as e.g. @code{xcms}).")
(properties `((upstream-name . "BiocIO")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)))
+ (list r-biocgenerics r-s4vectors))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocIO")
(synopsis "Standard input and output for Bioconductor packages")
(description
@@ -13545,10 +13250,7 @@ as well as local access. Developers can register a file extension, e.g.,
(properties `((upstream-name . "msmsEDA")))
(build-system r-build-system)
(propagated-inputs
- `(("r-gplots" ,r-gplots)
- ("r-mass" ,r-mass)
- ("r-msnbase" ,r-msnbase)
- ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (list r-gplots r-mass r-msnbase r-rcolorbrewer))
(home-page
"https://bioconductor.org/packages/msmsEDA")
(synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
@@ -13571,10 +13273,7 @@ experiments, and visualize de influence of the involved factors.")
(properties `((upstream-name . "msmsTests")))
(build-system r-build-system)
(propagated-inputs
- `(("r-edger" ,r-edger)
- ("r-msmseda" ,r-msmseda)
- ("r-msnbase" ,r-msnbase)
- ("r-qvalue" ,r-qvalue)))
+ (list r-edger r-msmseda r-msnbase r-qvalue))
(home-page
"https://bioconductor.org/packages/msmsTests")
(synopsis "Differential LC-MS/MS expression tests")
@@ -13603,34 +13302,34 @@ relevant, and the minimum expression of the most abundant condition.")
(properties `((upstream-name . "CATALYST")))
(build-system r-build-system)
(propagated-inputs
- `(("r-circlize" ,r-circlize)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-consensusclusterplus" ,r-consensusclusterplus)
- ("r-cowplot" ,r-cowplot)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-drc" ,r-drc)
- ("r-flowcore" ,r-flowcore)
- ("r-flowsom" ,r-flowsom)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-ggridges" ,r-ggridges)
- ("r-gridextra" ,r-gridextra)
- ("r-magrittr" ,r-magrittr)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-nnls" ,r-nnls)
- ("r-purrr" ,r-purrr)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape2" ,r-reshape2)
- ("r-rtsne" ,r-rtsne)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-scater" ,r-scater)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-circlize
+ r-complexheatmap
+ r-consensusclusterplus
+ r-cowplot
+ r-data-table
+ r-dplyr
+ r-drc
+ r-flowcore
+ r-flowsom
+ r-ggplot2
+ r-ggrepel
+ r-ggridges
+ r-gridextra
+ r-magrittr
+ r-matrix
+ r-matrixstats
+ r-nnls
+ r-purrr
+ r-rcolorbrewer
+ r-reshape2
+ r-rtsne
+ r-s4vectors
+ r-scales
+ r-scater
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page
"https://github.com/HelenaLC/CATALYST")
(synopsis "Cytometry data analysis tools")
@@ -13660,22 +13359,22 @@ standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
"0pb9ar1wy613vg6sfdmn8n4cfv1328m8bagnigsjdb3hc3hbir4z"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-homo-sapiens" ,r-homo-sapiens)
- ("r-iranges" ,r-iranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-genomeinfodb
+ r-genomicfiles
+ r-genomicranges
+ r-ggplot2
+ r-homo-sapiens
+ r-iranges
+ r-rtracklayer
+ r-s4vectors
+ r-shiny
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/erma")
(synopsis "Epigenomic road map adventures")
(description
@@ -13710,35 +13409,35 @@ by Ernst and Kellis.")
(("fechable") "fetchable"))
#t)))))
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationfilter" ,r-annotationfilter)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-bsgenome" ,r-bsgenome)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggally" ,r-ggally)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gridextra" ,r-gridextra)
- ("r-gtable" ,r-gtable)
- ("r-hmisc" ,r-hmisc)
- ("r-iranges" ,r-iranges)
- ("r-organismdbi" ,r-organismdbi)
- ("r-reshape2" ,r-reshape2)
- ("r-rlang" ,r-rlang)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationfilter
+ r-biobase
+ r-biocgenerics
+ r-biostrings
+ r-biovizbase
+ r-bsgenome
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-ggally
+ r-ggplot2
+ r-gridextra
+ r-gtable
+ r-hmisc
+ r-iranges
+ r-organismdbi
+ r-reshape2
+ r-rlang
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-scales
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "http://www.tengfei.name/ggbio/")
(synopsis "Visualization tools for genomic data")
(description
@@ -13776,21 +13475,21 @@ interval to data view, mismatch pileup, and several splicing summaries.")
(("importFrom\\(ff,.*") "import(ff)\n"))
#t)))))
(propagated-inputs
- `(("r-batchjobs" ,r-batchjobs)
- ("r-bbmisc" ,r-bbmisc)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-bit" ,r-bit)
- ("r-doparallel" ,r-doparallel)
- ("r-ff" ,r-ff)
- ("r-ffbase" ,r-ffbase)
- ("r-foreach" ,r-foreach)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-batchjobs
+ r-bbmisc
+ r-biocgenerics
+ r-bit
+ r-doparallel
+ r-ff
+ r-ffbase
+ r-foreach
+ r-genomicfiles
+ r-genomicranges
+ r-rtracklayer
+ r-s4vectors
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/gQTLBase")
(synopsis "Infrastructure for eQTL, mQTL and similar studies")
(description
@@ -13813,38 +13512,38 @@ and more.")
(properties `((upstream-name . "gQTLstats")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-batchjobs" ,r-batchjobs)
- ("r-bbmisc" ,r-bbmisc)
- ("r-beeswarm" ,r-beeswarm)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-doparallel" ,r-doparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-erma" ,r-erma)
- ("r-ffbase" ,r-ffbase)
- ("r-foreach" ,r-foreach)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-gqtlbase" ,r-gqtlbase)
- ("r-hardyweinberg" ,r-hardyweinberg)
- ("r-homo-sapiens" ,r-homo-sapiens)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-mgcv" ,r-mgcv)
- ("r-plotly" ,r-plotly)
- ("r-reshape2" ,r-reshape2)
- ("r-s4vectors" ,r-s4vectors)
- ("r-shiny" ,r-shiny)
- ("r-snpstats" ,r-snpstats)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-batchjobs
+ r-bbmisc
+ r-beeswarm
+ r-biobase
+ r-biocgenerics
+ r-doparallel
+ r-dplyr
+ r-erma
+ r-ffbase
+ r-foreach
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicfiles
+ r-genomicranges
+ r-ggbeeswarm
+ r-ggplot2
+ r-gqtlbase
+ r-hardyweinberg
+ r-homo-sapiens
+ r-iranges
+ r-limma
+ r-mgcv
+ r-plotly
+ r-reshape2
+ r-s4vectors
+ r-shiny
+ r-snpstats
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/gQTLstats")
(synopsis "Computationally efficient analysis for eQTL and allied studies")
(description
@@ -13869,30 +13568,30 @@ family of feature/genome hypotheses.")
(properties `((upstream-name . "Gviz")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-biovizbase" ,r-biovizbase)
- ("r-bsgenome" ,r-bsgenome)
- ("r-digest" ,r-digest)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-lattice" ,r-lattice)
- ("r-latticeextra" ,r-latticeextra)
- ("r-matrixstats" ,r-matrixstats)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-xvector" ,r-xvector)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-biobase
+ r-biocgenerics
+ r-biomart
+ r-biostrings
+ r-biovizbase
+ r-bsgenome
+ r-digest
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-lattice
+ r-latticeextra
+ r-matrixstats
+ r-rcolorbrewer
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-xvector))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/Gviz")
(synopsis "Plotting data and annotation information along genomic coordinates")
(description
@@ -13917,20 +13616,20 @@ with your data.")
"0s67jgk3gnfiyfjwhq4r5xlfnip29blis4fg75kn4qmvjv5j2pxx"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-readr" ,r-readr)
- ("r-s4vectors" ,r-s4vectors)
- ("r-snpstats" ,r-snpstats)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationhub
+ r-biocfilecache
+ r-biostrings
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-readr
+ r-s4vectors
+ r-snpstats
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/gwascat")
(synopsis "Tools for data in the EMBL-EBI GWAS catalog")
(description
@@ -13951,10 +13650,7 @@ EMBL-EBI GWAS catalog.")
(properties `((upstream-name . "KEGGgraph")))
(build-system r-build-system)
(propagated-inputs
- `(("r-graph" ,r-graph)
- ("r-rcurl" ,r-rcurl)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-xml" ,r-xml)))
+ (list r-graph r-rcurl r-rgraphviz r-xml))
(home-page "https://bioconductor.org/packages/KEGGgraph")
(synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
(description
@@ -13978,18 +13674,18 @@ functionalities including parsing, graph operation, visualization and etc.")
"1v9b372d5hpwwik6956mfwc9b3bibygz042i4nydsklnbwm5vcmg"))))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfiles" ,r-genomicfiles)
- ("r-httr" ,r-httr)
- ("r-matrix" ,r-matrix)
- ("r-rsamtools" ,r-rsamtools)
- ("r-snpstats" ,r-snpstats)
- ("r-variantannotation" ,r-variantannotation)))
+ (list r-biocgenerics
+ r-ensdb-hsapiens-v75
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicfiles
+ r-httr
+ r-matrix
+ r-rsamtools
+ r-snpstats
+ r-variantannotation))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ldblock")
(synopsis "Data structures for linkage disequilibrium measures in populations")
(description
@@ -14015,9 +13711,7 @@ defining LD blocks.")
(properties `((upstream-name . "LDheatmap")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genetics" ,r-genetics)
- ("r-rcpp" ,r-rcpp)
- ("r-snpstats" ,r-snpstats)))
+ (list r-genetics r-rcpp r-snpstats))
(home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
(synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
(description
@@ -14042,14 +13736,14 @@ on the plot.")
"1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw"))))
(build-system r-build-system)
(inputs
- `(("gsl" ,gsl)))
- (propagated-inputs
- `(("r-lme4" ,r-lme4)
- ("r-nnet" ,r-nnet)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-rjags" ,r-rjags)))
+ (list gsl))
+ (propagated-inputs
+ (list r-lme4
+ r-nnet
+ r-rcpp
+ r-rcpparmadillo
+ r-rgraphviz
+ r-rjags))
(home-page "https://r-bayesian-networks.org/")
(synopsis "Modelling multivariate data with additive bayesian networks")
(description
@@ -14079,12 +13773,9 @@ statistical dependencies in messy, complex data.")
"08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
(build-system r-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(propagated-inputs
- `(("r-bh" ,r-bh)
- ("r-catools" ,r-catools)
- ("r-rcpp" ,r-rcpp)
- ("r-rsamtools" ,r-rsamtools)))
+ (list r-bh r-catools r-rcpp r-rsamtools))
(home-page "https://cran.r-project.org/web/packages/spp/")
(synopsis "ChIP-Seq processing pipeline")
(description "This package provides tools for analysis of ChIP-seq and
@@ -14104,14 +13795,14 @@ other functional sequencing data.")
(properties `((upstream-name . "pathview")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-graph" ,r-graph)
- ("r-kegggraph" ,r-kegggraph)
- ("r-keggrest" ,r-keggrest)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-png" ,r-png)
- ("r-rgraphviz" ,r-rgraphviz)
- ("r-xml" ,r-xml)))
+ (list r-annotationdbi
+ r-graph
+ r-kegggraph
+ r-keggrest
+ r-org-hs-eg-db
+ r-png
+ r-rgraphviz
+ r-xml))
(home-page "https://pathview.uncc.edu/")
(synopsis "Tool set for pathway based data integration and visualization")
(description
@@ -14138,12 +13829,9 @@ large-scale and fully automated analysis.")
"0ha34b5cg26940xihgky45adns1nflrgq2qjq77w4bncxpaacsqq"))))
(properties `((upstream-name . "snpStats")))
(build-system r-build-system)
- (inputs `(("zlib" ,zlib)))
+ (inputs (list zlib))
(propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-matrix" ,r-matrix)
- ("r-survival" ,r-survival)
- ("r-zlibbioc" ,r-zlibbioc)))
+ (list r-biocgenerics r-matrix r-survival r-zlibbioc))
(home-page "https://bioconductor.org/packages/snpStats")
(synopsis "Methods for SNP association studies")
(description
@@ -14166,21 +13854,21 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.")
(properties `((upstream-name . "chromstaR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-bamsignals" ,r-bamsignals)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-chromstardata" ,r-chromstardata)
- ("r-doparallel" ,r-doparallel)
- ("r-foreach" ,r-foreach)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicalignments" ,r-genomicalignments)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-mvtnorm" ,r-mvtnorm)
- ("r-reshape2" ,r-reshape2)
- ("r-rsamtools" ,r-rsamtools)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-bamsignals
+ r-biocgenerics
+ r-chromstardata
+ r-doparallel
+ r-foreach
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-mvtnorm
+ r-reshape2
+ r-rsamtools
+ r-s4vectors))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/ataudt/chromstaR")
(synopsis "Chromatin state analysis for ChIP-Seq data")
(description
@@ -14204,16 +13892,16 @@ analyses.")
(properties `((upstream-name . "Guitar")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-dplyr" ,r-dplyr)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-knitr" ,r-knitr)
- ("r-magrittr" ,r-magrittr)
- ("r-rtracklayer" ,r-rtracklayer)))
+ (list r-annotationdbi
+ r-dplyr
+ r-genomicfeatures
+ r-genomicranges
+ r-ggplot2
+ r-knitr
+ r-magrittr
+ r-rtracklayer))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/Guitar")
(synopsis "Visualize genomic features")
(description
@@ -14235,8 +13923,7 @@ starting site, start codon, stop codon and transcription ending site.")
(properties `((upstream-name . "Sushi")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biomart" ,r-biomart)
- ("r-zoo" ,r-zoo)))
+ (list r-biomart r-zoo))
(home-page "https://bioconductor.org/packages/Sushi")
(synopsis "Tools for visualizing genomics data")
(description
@@ -14258,17 +13945,17 @@ visualizations for publication-quality multi-panel figures.")
(properties `((upstream-name . "ballgown")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-sva" ,r-sva)))
+ (list r-biobase
+ r-genomeinfodb
+ r-genomicranges
+ r-iranges
+ r-limma
+ r-rcolorbrewer
+ r-rtracklayer
+ r-s4vectors
+ r-sva))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/ballgown")
(synopsis "Flexible, isoform-level differential expression analysis")
(description
@@ -14291,17 +13978,17 @@ to annotation.")
"0mg7n3990qv65rg624473ssccka0yjpgc20glrdc5saci891j44r"))))
(properties `((upstream-name . "megadepth")))
(build-system r-build-system)
- (inputs `(("megadepth" ,megadepth)))
+ (inputs (list megadepth))
(propagated-inputs
- `(("r-cmdfun" ,r-cmdfun)
- ("r-dplyr" ,r-dplyr)
- ("r-fs" ,r-fs)
- ("r-genomicranges" ,r-genomicranges)
- ("r-magrittr" ,r-magrittr)
- ("r-readr" ,r-readr)
- ("r-xfun" ,r-xfun)))
+ (list r-cmdfun
+ r-dplyr
+ r-fs
+ r-genomicranges
+ r-magrittr
+ r-readr
+ r-xfun))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/LieberInstitute/megadepth")
(synopsis "BigWig and BAM related utilities")
(description
@@ -14325,16 +14012,16 @@ regions or annotations of your choice from BigWig files.")
(properties `((upstream-name . "BEclear")))
(build-system r-build-system)
(propagated-inputs
- `(("r-abind" ,r-abind)
- ("r-biocparallel" ,r-biocparallel)
- ("r-data-table" ,r-data-table)
- ("r-futile-logger" ,r-futile-logger)
- ("r-matrix" ,r-matrix)
- ("r-outliers" ,r-outliers)
- ("r-rcpp" ,r-rcpp)
- ("r-rdpack" ,r-rdpack)))
+ (list r-abind
+ r-biocparallel
+ r-data-table
+ r-futile-logger
+ r-matrix
+ r-outliers
+ r-rcpp
+ r-rdpack))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/uds-helms/BEclear")
(synopsis "Correction of batch effects in DNA methylation data")
(description
@@ -14358,19 +14045,19 @@ real numbers.")
(properties `((upstream-name . "BgeeCall")))
(build-system r-build-system)
(propagated-inputs
- `(("kallisto" ,kallisto)
- ("r-biomart" ,r-biomart)
- ("r-biostrings" ,r-biostrings)
- ("r-data-table" ,r-data-table)
- ("r-dplyr" ,r-dplyr)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-jsonlite" ,r-jsonlite)
- ("r-rhdf5" ,r-rhdf5)
- ("r-rslurm" ,r-rslurm)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-sjmisc" ,r-sjmisc)
- ("r-tximport" ,r-tximport)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list kallisto
+ r-biomart
+ r-biostrings
+ r-data-table
+ r-dplyr
+ r-genomicfeatures
+ r-jsonlite
+ r-rhdf5
+ r-rslurm
+ r-rtracklayer
+ r-sjmisc
+ r-tximport))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/BgeeDB/BgeeCall")
(synopsis "RNA-Seq present/absent gene expression calls generation")
(description
@@ -14394,18 +14081,18 @@ all RNA-Seq libraries of each species integrated in Bgee.")
(properties `((upstream-name . "BgeeDB")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-curl" ,r-curl)
- ("r-data-table" ,r-data-table)
- ("r-digest" ,r-digest)
- ("r-dplyr" ,r-dplyr)
- ("r-graph" ,r-graph)
- ("r-r-utils" ,r-r-utils)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-tidyr" ,r-tidyr)
- ("r-topgo" ,r-topgo)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-curl
+ r-data-table
+ r-digest
+ r-dplyr
+ r-graph
+ r-r-utils
+ r-rcurl
+ r-rsqlite
+ r-tidyr
+ r-topgo))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/BgeeDB/BgeeDB_R")
(synopsis "Annotation and gene expression data retrieval from Bgee database")
(description
@@ -14428,11 +14115,8 @@ anatomical terms, mapped to genes by expression patterns.")
(properties `((upstream-name . "biobtreeR")))
(build-system r-build-system)
(propagated-inputs
- `(("r-httpuv" ,r-httpuv)
- ("r-httr" ,r-httr)
- ("r-jsonlite" ,r-jsonlite)
- ("r-stringi" ,r-stringi)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-httpuv r-httr r-jsonlite r-stringi))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/tamerh/biobtreeR")
(synopsis "Use biobtree tool from R")
(description
@@ -14455,7 +14139,7 @@ mappings functionalities.")
(properties `((upstream-name . "minet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-infotheo" ,r-infotheo)))
+ (list r-infotheo))
(home-page "http://minet.meyerp.com")
(synopsis "Mutual information networks")
(description
@@ -14478,10 +14162,7 @@ information networks from data.")
`((upstream-name . "geNetClassifier")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-e1071" ,r-e1071)
- ("r-ebarrays" ,r-ebarrays)
- ("r-minet" ,r-minet)))
+ (list r-biobase r-e1071 r-ebarrays r-minet))
(home-page "https://www.cicancer.org")
(synopsis "Classify diseases and build gene networks using expression profiles")
(description
@@ -14504,8 +14185,8 @@ interface to query the classifier.")
"1bwmlxmizhmim2l0mk406hxfr5mnmsg5zbqkjyygaipa971m9s00"))))
(properties `((upstream-name . "dir.expiry")))
(build-system r-build-system)
- (propagated-inputs `(("r-filelock" ,r-filelock)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (propagated-inputs (list r-filelock))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/dir.expiry")
(synopsis "Managing expiration for cache directories")
(description
@@ -14530,8 +14211,8 @@ eliminating obsolete caches generated by old versions of packages.")
`((upstream-name . "basilisk.utils")))
(build-system r-build-system)
(propagated-inputs
- `(("r-dir-expiry" ,r-dir-expiry)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-dir-expiry))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/basilisk.utils")
(synopsis "Basilisk installation utilities")
(description
@@ -14553,10 +14234,8 @@ package, primarily for creation of the underlying Conda instance.")
(properties `((upstream-name . "basilisk")))
(build-system r-build-system)
(propagated-inputs
- `(("r-basilisk-utils" ,r-basilisk-utils)
- ("r-dir-expiry" ,r-dir-expiry)
- ("r-reticulate" ,r-reticulate)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-basilisk-utils r-dir-expiry r-reticulate))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/basilisk")
(synopsis "Freeze Python dependencies inside Bioconductor packages")
(description
@@ -14586,13 +14265,13 @@ Python environments in a single R session.")
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- `(("r-biocmanager" ,r-biocmanager)
- ("r-fs" ,r-fs)
- ("r-glue" ,r-glue)
- ("r-rlang" ,r-rlang)
- ("r-styler" ,r-styler)
- ("r-usethis" ,r-usethis)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocmanager
+ r-fs
+ r-glue
+ r-rlang
+ r-styler
+ r-usethis))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/lcolladotor/biocthis")
(synopsis "Automate package and project setup for Bioconductor packages")
(description
@@ -14616,13 +14295,13 @@ Bioconductor-friendly.")
`((upstream-name . "BiocDockerManager")))
(build-system r-build-system)
(propagated-inputs
- `(("docker" ,docker)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-memoise" ,r-memoise)
- ("r-readr" ,r-readr)
- ("r-whisker" ,r-whisker)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list docker
+ r-dplyr
+ r-httr
+ r-memoise
+ r-readr
+ r-whisker))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/BiocDockerManager")
(synopsis "Access and manage Bioconductor Docker images")
(description
@@ -14645,25 +14324,25 @@ the Bioconductor project.")
(properties `((upstream-name . "biodb")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocfilecache" ,r-biocfilecache)
- ("r-chk" ,r-chk)
- ("r-jsonlite" ,r-jsonlite)
- ("r-lgr" ,r-lgr)
- ("r-lifecycle" ,r-lifecycle)
- ("r-openssl" ,r-openssl)
- ("r-plyr" ,r-plyr)
- ("r-progress" ,r-progress)
- ("r-r6" ,r-r6)
- ("r-rappdirs" ,r-rappdirs)
- ("r-rcpp" ,r-rcpp)
- ("r-rcurl" ,r-rcurl)
- ("r-rsqlite" ,r-rsqlite)
- ("r-stringr" ,r-stringr)
- ("r-testthat" ,r-testthat)
- ("r-withr" ,r-withr)
- ("r-xml" ,r-xml)
- ("r-yaml" ,r-yaml)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-biocfilecache
+ r-chk
+ r-jsonlite
+ r-lgr
+ r-lifecycle
+ r-openssl
+ r-plyr
+ r-progress
+ r-r6
+ r-rappdirs
+ r-rcpp
+ r-rcurl
+ r-rsqlite
+ r-stringr
+ r-testthat
+ r-withr
+ r-xml
+ r-yaml))
+ (native-inputs (list r-knitr))
(home-page "https://bioconductor.org/packages/biodb")
(synopsis "Library for connecting to chemical and biological databases")
(description
@@ -14690,11 +14369,8 @@ separate published packages.")
(properties `((upstream-name . "biomformat")))
(build-system r-build-system)
(propagated-inputs
- `(("r-jsonlite" ,r-jsonlite)
- ("r-matrix" ,r-matrix)
- ("r-plyr" ,r-plyr)
- ("r-rhdf5" ,r-rhdf5)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-jsonlite r-matrix r-plyr r-rhdf5))
+ (native-inputs (list r-knitr))
(home-page "https://github.com/joey711/biomformat/")
(synopsis "Interface package for the BIOM file format")
(description
@@ -14742,10 +14418,7 @@ design.")
(properties `((upstream-name . "BioMVCClass")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-graph" ,r-graph)
- ("r-mvcclass" ,r-mvcclass)
- ("r-rgraphviz" ,r-rgraphviz)))
+ (list r-biobase r-graph r-mvcclass r-rgraphviz))
(home-page "https://bioconductor.org/packages/BioMVCClass")
(synopsis "Model-View-Controller (MVC) classes that use Biobase")
(description
@@ -14767,10 +14440,7 @@ design.")
(properties `((upstream-name . "biomvRCNS")))
(build-system r-build-system)
(propagated-inputs
- `(("r-genomicranges" ,r-genomicranges)
- ("r-gviz" ,r-gviz)
- ("r-iranges" ,r-iranges)
- ("r-mvtnorm" ,r-mvtnorm)))
+ (list r-genomicranges r-gviz r-iranges r-mvtnorm))
(home-page "https://bioconductor.org/packages/biomvRCNS")
(synopsis "Copy number study and segmentation for multivariate biological data")
(description
@@ -14795,28 +14465,28 @@ using aCGH or sequencing.")
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-complexheatmap" ,r-complexheatmap)
- ("r-deseq2" ,r-deseq2)
- ("r-dynamictreecut" ,r-dynamictreecut)
- ("r-genie3" ,r-genie3)
- ("r-ggnetwork" ,r-ggnetwork)
- ("r-ggnewscale" ,r-ggnewscale)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggpubr" ,r-ggpubr)
- ("r-igraph" ,r-igraph)
- ("r-intergraph" ,r-intergraph)
- ("r-matrixstats" ,r-matrixstats)
- ("r-minet" ,r-minet)
- ("r-netrep" ,r-netrep)
- ("r-networkd3" ,r-networkd3)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-reshape2" ,r-reshape2)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-sva" ,r-sva)
- ("r-wgcna" ,r-wgcna)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocparallel
+ r-complexheatmap
+ r-deseq2
+ r-dynamictreecut
+ r-genie3
+ r-ggnetwork
+ r-ggnewscale
+ r-ggplot2
+ r-ggpubr
+ r-igraph
+ r-intergraph
+ r-matrixstats
+ r-minet
+ r-netrep
+ r-networkd3
+ r-rcolorbrewer
+ r-reshape2
+ r-summarizedexperiment
+ r-sva
+ r-wgcna))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/almeidasilvaf/BioNERO")
(synopsis "Biological network reconstruction omnibus")
(description
@@ -14851,11 +14521,7 @@ networks.")
(properties `((upstream-name . "BioNet")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-graph" ,r-graph)
- ("r-igraph" ,r-igraph)
- ("r-rbgl" ,r-rbgl)))
+ (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
(home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
(synopsis "Functional analysis of biological networks")
(description
@@ -14884,26 +14550,26 @@ scoring subnetwork.")
(properties `((upstream-name . "BioNetStat")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-dt" ,r-dt)
- ("r-ggplot2" ,r-ggplot2)
- ("r-hmisc" ,r-hmisc)
- ("r-igraph" ,r-igraph)
- ("r-knitr" ,r-knitr)
- ("r-markdown" ,r-markdown)
- ("r-pathview" ,r-pathview)
- ("r-pheatmap" ,r-pheatmap)
- ("r-plyr" ,r-plyr)
- ("r-psych" ,r-psych)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rjsonio" ,r-rjsonio)
- ("r-rmarkdown" ,r-rmarkdown)
- ("r-shiny" ,r-shiny)
- ("r-shinybs" ,r-shinybs)
- ("r-whisker" ,r-whisker)
- ("r-yaml" ,r-yaml)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biocparallel
+ r-dt
+ r-ggplot2
+ r-hmisc
+ r-igraph
+ r-knitr
+ r-markdown
+ r-pathview
+ r-pheatmap
+ r-plyr
+ r-psych
+ r-rcolorbrewer
+ r-rjsonio
+ r-rmarkdown
+ r-shiny
+ r-shinybs
+ r-whisker
+ r-yaml))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/jardimViniciusC/BioNetStat")
(synopsis "Biological network analysis")
(description
@@ -14926,11 +14592,9 @@ network and metabolic pathways view.")
(properties `((upstream-name . "BioQC")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-edger" ,r-edger)
- ("r-rcpp" ,r-rcpp)))
+ (list r-biobase r-edger r-rcpp))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://accio.github.io/BioQC/")
(synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
(description
@@ -14954,15 +14618,15 @@ optimised for high performance.")
(properties `((upstream-name . "BioTIP")))
(build-system r-build-system)
(propagated-inputs
- `(("r-cluster" ,r-cluster)
- ("r-genomicranges" ,r-genomicranges)
- ("r-hmisc" ,r-hmisc)
- ("r-igraph" ,r-igraph)
- ("r-mass" ,r-mass)
- ("r-psych" ,r-psych)
- ("r-stringr" ,r-stringr)))
+ (list r-cluster
+ r-genomicranges
+ r-hmisc
+ r-igraph
+ r-mass
+ r-psych
+ r-stringr))
(native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-knitr))
(home-page "https://github.com/xyang2uchicago/BioTIP")
(synopsis "R package for characterization of biological tipping-point")
(description
@@ -14984,20 +14648,20 @@ help unravel disease regulatory trajectory.")
(properties `((upstream-name . "biotmle")))
(build-system r-build-system)
(propagated-inputs
- `(("r-assertthat" ,r-assertthat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-dplyr" ,r-dplyr)
- ("r-drtmle" ,r-drtmle)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggsci" ,r-ggsci)
- ("r-limma" ,r-limma)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-superheat" ,r-superheat)
- ("r-tibble" ,r-tibble)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-assertthat
+ r-biocgenerics
+ r-biocparallel
+ r-dplyr
+ r-drtmle
+ r-ggplot2
+ r-ggsci
+ r-limma
+ r-s4vectors
+ r-summarizedexperiment
+ r-superheat
+ r-tibble))
+ (native-inputs
+ (list r-knitr))
(home-page "https://code.nimahejazi.org/biotmle/")
(synopsis "Targeted learning with moderated statistics for biomarker discovery")
(description
@@ -15026,31 +14690,31 @@ ensemble machine learning for the estimation of nuisance functions.")
(properties `((upstream-name . "bsseq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biostrings" ,r-biostrings)
- ("r-bsgenome" ,r-bsgenome)
- ("r-data-table" ,r-data-table)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-hdf5array" ,r-hdf5array)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-locfit" ,r-locfit)
- ("r-permute" ,r-permute)
- ("r-r-utils" ,r-r-utils)
- ("r-rcpp" ,r-rcpp)
- ("r-rhdf5" ,r-rhdf5)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scales" ,r-scales)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-beachmat
+ r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biostrings
+ r-bsgenome
+ r-data-table
+ r-delayedarray
+ r-delayedmatrixstats
+ r-genomeinfodb
+ r-genomicranges
+ r-gtools
+ r-hdf5array
+ r-iranges
+ r-limma
+ r-locfit
+ r-permute
+ r-r-utils
+ r-rcpp
+ r-rhdf5
+ r-s4vectors
+ r-scales
+ r-summarizedexperiment))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/hansenlab/bsseq")
(synopsis "Analyze, manage and store bisulfite sequencing data")
(description
@@ -15072,25 +14736,25 @@ visualizing bisulfite sequencing data.")
(properties `((upstream-name . "dmrseq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationhub" ,r-annotationhub)
- ("r-annotatr" ,r-annotatr)
- ("r-biocparallel" ,r-biocparallel)
- ("r-bsseq" ,r-bsseq)
- ("r-bumphunter" ,r-bumphunter)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-ggplot2" ,r-ggplot2)
- ("r-iranges" ,r-iranges)
- ("r-locfit" ,r-locfit)
- ("r-matrixstats" ,r-matrixstats)
- ("r-nlme" ,r-nlme)
- ("r-outliers" ,r-outliers)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationhub
+ r-annotatr
+ r-biocparallel
+ r-bsseq
+ r-bumphunter
+ r-delayedmatrixstats
+ r-genomeinfodb
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-locfit
+ r-matrixstats
+ r-nlme
+ r-outliers
+ r-rcolorbrewer
+ r-rtracklayer
+ r-s4vectors))
+ (native-inputs
+ (list r-knitr))
(home-page "https://bioconductor.org/packages/dmrseq")
(synopsis "Detection and inference of differentially methylated regions")
(description
@@ -15122,30 +14786,30 @@ interest on transformed methylation proportions.")
(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp"))))))
(propagated-inputs
- `(("r-checkmate" ,r-checkmate)
- ("r-crayon" ,r-crayon)
- ("r-curl" ,r-curl)
- ("r-digest" ,r-digest)
- ("r-dplyr" ,r-dplyr)
- ("r-httr" ,r-httr)
- ("r-igraph" ,r-igraph)
- ("r-jsonlite" ,r-jsonlite)
- ("r-later" ,r-later)
- ("r-logger" ,r-logger)
- ("r-magrittr" ,r-magrittr)
- ("r-progress" ,r-progress)
- ("r-purrr" ,r-purrr)
- ("r-rappdirs" ,r-rappdirs)
- ("r-readr" ,r-readr)
- ("r-readxl" ,r-readxl)
- ("r-rlang" ,r-rlang)
- ("r-stringr" ,r-stringr)
- ("r-tibble" ,r-tibble)
- ("r-tidyr" ,r-tidyr)
- ("r-tidyselect" ,r-tidyselect)
- ("r-xml2" ,r-xml2)
- ("r-yaml" ,r-yaml)))
- (native-inputs `(("r-knitr" ,r-knitr)))
+ (list r-checkmate
+ r-crayon
+ r-curl
+ r-digest
+ r-dplyr
+ r-httr
+ r-igraph
+ r-jsonlite
+ r-later
+ r-logger
+ r-magrittr
+ r-progress
+ r-purrr
+ r-rappdirs
+ r-readr
+ r-readxl
+ r-rlang
+ r-stringr
+ r-tibble
+ r-tidyr
+ r-tidyselect
+ r-xml2
+ r-yaml))
+ (native-inputs (list r-knitr))
(home-page "https://saezlab.github.io/OmnipathR/")
(synopsis "OmniPath web service client and more")
(description
@@ -15170,34 +14834,34 @@ for ligand activity prediction from transcriptomics data.")
(properties `((upstream-name . "biscuiteer")))
(build-system r-build-system)
(propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biscuiteerdata" ,r-biscuiteerdata)
- ("r-bsseq" ,r-bsseq)
- ("r-data-table" ,r-data-table)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dmrseq" ,r-dmrseq)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-gtools" ,r-gtools)
- ("r-hdf5array" ,r-hdf5array)
- ("r-homo-sapiens" ,r-homo-sapiens)
- ("r-impute" ,r-impute)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-mus-musculus" ,r-mus-musculus)
- ("r-qdnaseq" ,r-qdnaseq)
- ("r-qualv" ,r-qualv)
- ("r-r-utils" ,r-r-utils)
- ("r-readr" ,r-readr)
- ("r-rsamtools" ,r-rsamtools)
- ("r-rtracklayer" ,r-rtracklayer)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-variantannotation" ,r-variantannotation)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-biobase
+ r-biocgenerics
+ r-biocparallel
+ r-biscuiteerdata
+ r-bsseq
+ r-data-table
+ r-delayedmatrixstats
+ r-dmrseq
+ r-genomeinfodb
+ r-genomicranges
+ r-gtools
+ r-hdf5array
+ r-homo-sapiens
+ r-impute
+ r-matrix
+ r-matrixstats
+ r-mus-musculus
+ r-qdnaseq
+ r-qualv
+ r-r-utils
+ r-readr
+ r-rsamtools
+ r-rtracklayer
+ r-s4vectors
+ r-summarizedexperiment
+ r-variantannotation))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/trichelab/biscuiteer")
(synopsis "Convenience functions for the Biscuit package")
(description
@@ -15221,23 +14885,23 @@ estimates, etc.")
(properties `((upstream-name . "tximeta")))
(build-system r-build-system)
(propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-annotationhub" ,r-annotationhub)
- ("r-biocfilecache" ,r-biocfilecache)
- ("r-biostrings" ,r-biostrings)
- ("r-ensembldb" ,r-ensembldb)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicfeatures" ,r-genomicfeatures)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-jsonlite" ,r-jsonlite)
- ("r-matrix" ,r-matrix)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-tibble" ,r-tibble)
- ("r-tximport" ,r-tximport)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-annotationdbi
+ r-annotationhub
+ r-biocfilecache
+ r-biostrings
+ r-ensembldb
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-jsonlite
+ r-matrix
+ r-s4vectors
+ r-summarizedexperiment
+ r-tibble
+ r-tximport))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/mikelove/tximeta")
(synopsis "Transcript quantification import with automatic metadata")
(description
@@ -15261,24 +14925,24 @@ reproducibility.")
(properties `((upstream-name . "phyloseq")))
(build-system r-build-system)
(propagated-inputs
- `(("r-ade4" ,r-ade4)
- ("r-ape" ,r-ape)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biomformat" ,r-biomformat)
- ("r-biostrings" ,r-biostrings)
- ("r-cluster" ,r-cluster)
- ("r-data-table" ,r-data-table)
- ("r-foreach" ,r-foreach)
- ("r-ggplot2" ,r-ggplot2)
- ("r-igraph" ,r-igraph)
- ("r-multtest" ,r-multtest)
- ("r-plyr" ,r-plyr)
- ("r-reshape2" ,r-reshape2)
- ("r-scales" ,r-scales)
- ("r-vegan" ,r-vegan)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
+ (list r-ade4
+ r-ape
+ r-biobase
+ r-biocgenerics
+ r-biomformat
+ r-biostrings
+ r-cluster
+ r-data-table
+ r-foreach
+ r-ggplot2
+ r-igraph
+ r-multtest
+ r-plyr
+ r-reshape2
+ r-scales
+ r-vegan))
+ (native-inputs
+ (list r-knitr))
(home-page "https://github.com/joey711/phyloseq")
(synopsis "Handling and analysis of high-throughput microbiome census data")
(description