diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 547 |
1 files changed, 523 insertions, 24 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d532360f7e..35a4db026f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -640,6 +640,50 @@ from several related annotation packages.") data.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylation450kmanifest + (package + (name "r-illuminahumanmethylation450kmanifest") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri + "IlluminaHumanMethylation450kmanifest" + version 'annotation)) + (sha256 + (base32 + "0qx75xwifrbkqmbkd8dhf44c34ibmbivqh7y8rvgrsizmi5ybcj1")))) + (properties `((upstream-name . "IlluminaHumanMethylation450kmanifest"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page + "https://bioconductor.org/packages/IlluminaHumanMethylation450kmanifest") + (synopsis "Annotation for Illumina's 450k methylation arrays") + (description "This package provides a manifest for Illumina's 450k array +data.") + (license license:artistic2.0))) + +(define-public r-illuminahumanmethylationepicanno-ilm10b4-hg19 + (package + (name "r-illuminahumanmethylationepicanno-ilm10b4-hg19") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri + "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" + version 'annotation)) + (sha256 + (base32 + "0687b4k8hwfc18qgdd9ypv1skp37jd204fszba0gmrv3dc92i09c")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b4.hg19"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page + "https://doi.org/doi:10.18129/B9.bioc.IlluminaHumanMethylationEPICanno.ilm10b4.hg19") + (synopsis "Annotation for Illumina's EPIC methylation arrays") + (description + "This is an annotation package for Illumina's EPIC methylation arrays.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -1392,6 +1436,26 @@ curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.") (license license:gpl3))) +(define-public r-champdata + (package + (name "r-champdata") + (version "2.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ChAMPdata" version 'experiment)) + (sha256 + (base32 + "0rz762szfl02h4d3dj7ckd41ji9mdsja8nxqw6fl086z337041zw")))) + (properties `((upstream-name . "ChAMPdata"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics r-genomicranges)) + (home-page "https://bioconductor.org/packages/ChAMPdata") + (synopsis "Data packages for ChAMP package") + (description + "This package provides datasets needed for ChAMP including a test dataset +and blood controls for CNA analysis.") + (license license:gpl3))) + (define-public r-chromstardata (package (name "r-chromstardata") @@ -1434,6 +1498,63 @@ display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.") (license license:gpl2))) +(define-public r-flowsorted-blood-450k + (package + (name "r-flowsorted-blood-450k") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "FlowSorted.Blood.450k" + version 'experiment)) + (sha256 + (base32 + "1ha9qsp5g3g2yhnk574x6xhg95bb29ywvmg3ns1c50z69v6wbraq")))) + (properties `((upstream-name . "FlowSorted.Blood.450k"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page "https://bioconductor.org/packages/FlowSorted.Blood.450k") + (synopsis + "Illumina HumanMethylation data on sorted blood cell populations") + (description + "This package provides raw data objects for the Illumina 450k DNA +methylation microarrays, and an object depicting which CpGs on the array are +associated with cell type.") + (license license:artistic2.0))) + +(define-public r-flowsorted-blood-epic + (package + (name "r-flowsorted-blood-epic") + (version "2.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "FlowSorted.Blood.EPIC" version + 'experiment)) + (sha256 + (base32 + "1vybj69jxnirqg6ik03q3pb1vv23z8mir7wpi2ys7iljf5ixzgl1")))) + (properties `((upstream-name . "FlowSorted.Blood.EPIC"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-experimenthub + r-genefilter + r-minfi + r-nlme + r-quadprog + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/immunomethylomics/FlowSorted.Blood.EPIC") + (synopsis + "Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells") + (description + "This package provides raw data objects to be used for blood cell +proportion estimation in minfi and similar packages. The +@code{FlowSorted.Blood.EPIC} object is based in samples assayed by Brock +Christensen and colleagues; for details see Salas et al. 2018. +https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.") + (license license:gpl3))) + (define-public r-genelendatabase (package (name "r-genelendatabase") @@ -1523,6 +1644,28 @@ cluster labels and labels identifying spiked in cells. Column metadata includes channel names, protein marker names, and protein marker classes.") (license license:expat))) +(define-public r-illumina450probevariants-db + (package + (name "r-illumina450probevariants-db") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Illumina450ProbeVariants.db" + version 'experiment)) + (sha256 + (base32 + "1c1iqxi17s1a1sa1vab2ma7pjq1dxal7ibsiahj66ys0pa4sm42p")))) + (properties `((upstream-name . "Illumina450ProbeVariants.db"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/Illumina450ProbeVariants.db") + (synopsis + "Variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes") + (description + "This package includes details on variants for each probe on the 450k +bead chip for each of the four populations (Asian, American, African and +European).") + (license license:gpl3))) + (define-public r-italicsdata (package (name "r-italicsdata") @@ -1565,6 +1708,79 @@ gene expression indicate a role for enhancer priming in immune response\", publi in Nature Genetics, January 2018.") (license license:gpl2+))) +(define-public r-minfidata + (package + (name "r-minfidata") + (version "0.44.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "minfiData" version 'experiment)) + (sha256 + (base32 + "15s3kc629m2c78vkidmp6kcc28sn1wzjzrxazmd8z7x8cdad3q4g")))) + (properties `((upstream-name . "minfiData"))) + (build-system r-build-system) + (propagated-inputs + (list r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminahumanmethylation450kmanifest + r-minfi)) + (home-page "https://bioconductor.org/packages/minfiData") + (synopsis "Example data for the Illumina Methylation 450k array") + (description + "This package provides data from 6 samples across 2 groups from 450k +methylation arrays.") + (license license:artistic2.0))) + +(define-public r-missmethyl + (package + (name "r-missmethyl") + (version "1.32.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "missMethyl" version)) + (sha256 + (base32 + "1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma")))) + (properties `((upstream-name . "missMethyl"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biasedurn + r-biobase + r-biocgenerics + r-genomicranges + r-go-db + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno-ilm10b4-hg19 + r-illuminahumanmethylationepicmanifest + r-iranges + r-limma + r-methylumi + r-minfi + r-org-hs-eg-db + r-ruv + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/missMethyl") + (synopsis "Analyzing Illumina HumanMethylation BeadChip data") + (description + "This is a package for normalization, testing for differential +variability and differential methylation and gene set testing for data from +Illumina's Infinium HumanMethylation arrays. The normalization procedure is +subset-quantile within-array normalization (SWAN), which allows Infinium I and +II type probes on a single array to be normalized together. The test for +differential variability is based on an empirical Bayes version of Levene's +test. Differential methylation testing is performed using RUV, which can +adjust for systematic errors of unknown origin in high-dimensional data by +using negative control probes. Gene ontology analysis is performed by taking +into account the number of probes per gene on the array, as well as taking +into account multi-gene associated probes.") + (license license:gpl2))) + (define-public r-msdata (package (name "r-msdata") @@ -2516,13 +2732,13 @@ problems.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.13.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n")))) + "06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -2761,13 +2977,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv")))) + "1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs @@ -4533,6 +4749,46 @@ spent loading the full derfinder package when running the F-statistics calculation in parallel.") (license license:artistic2.0))) +(define-public r-dmrcate + (package + (name "r-dmrcate") + (version "2.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DMRcate" version)) + (sha256 + (base32 + "0iphlsbam5fcxbj5j0cmqk3wz5ykwz0mvk3qbrhzxbpf2h4w2qib")))) + (properties `((upstream-name . "DMRcate"))) + (build-system r-build-system) + (propagated-inputs + (list r-bsseq + r-dss + r-edger + r-experimenthub + r-genomeinfodb + r-genomicranges + r-gviz + r-iranges + r-limma + r-minfi + r-missmethyl + r-plyr + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DMRcate") + (synopsis "Methylation array and sequencing spatial analysis methods") + (description + "This is a package for de novo identification and extraction of +@dfn{differentially methylated regions} (DMRs) from the human genome using +@dfn{Whole Genome Bisulfite Sequencing} (WGBS) and Illumina Infinium +Array (450K and EPIC) data. It provides functionality for filtering probes +possibly confounded by SNPs and cross-hybridisation. It includes +@code{GRanges} generation and plotting functions.") + ;; GPLv3 with additional liability disclaimer. + (license license:gpl3))) + (define-public r-drimseq (package (name "r-drimseq") @@ -4568,6 +4824,32 @@ makes available functions for visualization and exploration of the data and results.") (license license:gpl3+))) +(define-public r-dss + (package + (name "r-dss") + (version "2.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DSS" version)) + (sha256 + (base32 + "1qm0pq6495fn2zrbddaadb1w01ry76rg8mmbmxf3zws9pww48jgf")))) + (properties `((upstream-name . "DSS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/DSS") + (synopsis "Dispersion shrinkage for sequencing data") + (description + "DSS is an R library performing differential analysis for count-based +sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from +RNA-seq, and differentially methylated loci or regions (DML/DMRs) from +@dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion +shrinkage method for estimating the dispersion parameter from Gamma-Poisson or +Beta-Binomial distributions.") + ;; Any version of the GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-bluster (package (name "r-bluster") @@ -4763,6 +5045,28 @@ domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on qvalue from Bioconductor. +(define-public r-isva + (package + (name "r-isva") + (version "1.9") + (source (origin + (method url-fetch) + (uri (cran-uri "isva" version)) + (sha256 + (base32 + "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z")))) + (properties `((upstream-name . "isva"))) + (build-system r-build-system) + (propagated-inputs (list r-fastica r-jade r-qvalue)) + (home-page "https://cran.r-project.org/package=isva") + (synopsis "Independent surrogate variable analysis") + (description + "Independent Surrogate Variable Analysis is an algorithm for feature +selection in the presence of potential confounding factors (see Teschendorff +AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") + (license license:gpl2))) + (define-public r-italics (package (name "r-italics") @@ -4902,14 +5206,14 @@ mapping.") (define-public r-nmf (package (name "r-nmf") - (version "0.25") + (version "0.26") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0kdl7yz4v7pms6y2lff4x5w7pwkx54488qx0v539qmvcbxv1if98")))) + "1h1fpjnj6vjvi9ygxpfxs8k5bhly0aflr54zj88khgzkylp5ci4d")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs @@ -5239,14 +5543,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.40.1") + (version "1.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy")))) + "1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5388,13 +5692,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.54.0") + (version "2.54.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq")))) + "13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -5473,13 +5777,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.5") + (version "1.32.6") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir")))) + "1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5653,6 +5957,68 @@ genome data packages and support for efficient SNP representation.") analysis.") (license license:artistic2.0))) +(define-public r-champ + (package + (name "r-champ") + (version "2.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ChAMP" version)) + (sha256 + (base32 + "10ss0a3miqrx92vy1r1h5rv3mnjn4iyl32q86s0x59d3fvqp2cx1")))) + (properties `((upstream-name . "ChAMP"))) + (build-system r-build-system) + (propagated-inputs + (list r-bumphunter + r-champdata + r-combinat + r-dendextend + r-dmrcate + r-dnacopy + r-doparallel + r-dt + r-genomicranges + r-ggplot2 + r-globaltest + r-goseq + r-hmisc + r-illumina450probevariants-db + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno-ilm10b4-hg19 + r-illuminahumanmethylationepicmanifest + r-illuminaio + r-impute + r-isva + r-kpmt + r-limma + r-marray + r-matrixstats + r-minfi + r-missmethyl + r-plotly + r-plyr + r-preprocesscore + r-prettydoc + r-quadprog + r-qvalue + r-rcolorbrewer + r-rmarkdown + r-rpmm + r-shiny + r-shinythemes + r-sva + r-watermelon)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ChAMP") + (synopsis + "Chip analysis methylation pipeline for Illumina HumanMethylation450 and EPIC") + (description + "The package includes quality control metrics, a selection of +normalization methods and novel methods to identify differentially methylated +regions and to highlight copy number alterations.") + (license license:gpl3))) + (define-public r-chipseeker (package (name "r-chipseeker") @@ -6145,6 +6511,48 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-enmix + (package + (name "r-enmix") + (version "1.34.02") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ENmix" version)) + (sha256 + (base32 + "0rn541xfsxfdyzy3dn727bwrfpkgp12282lax7xg1j8584mk4pcf")))) + (properties `((upstream-name . "ENmix"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationhub + r-biobase + r-doparallel + r-dynamictreecut + r-experimenthub + r-foreach + r-genefilter + r-geneplotter + r-gplots + r-gtools + r-illuminaio + r-impute + r-iranges + r-matrixstats + r-minfi + r-preprocesscore + r-quadprog + r-rpmm + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/release/bioc/html/ENmix.html") + (synopsis + "Quality control and analysis tools for Illumina DNA methylation BeadChip") + (description + "This package provides tools for quality control, analysis and +visualization of Illumina DNA methylation array data.") + (license license:artistic2.0))) + (define-public r-ensembldb (package (name "r-ensembldb") @@ -6524,6 +6932,30 @@ profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.") (license license:gpl2))) +(define-public r-globaltest + (package + (name "r-globaltest") + (version "5.52.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "globaltest" version)) + (sha256 + (base32 + "1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb")))) + (properties `((upstream-name . "globaltest"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotate r-annotationdbi r-biobase r-survival)) + (home-page "https://bioconductor.org/packages/globaltest") + (synopsis + "Test groups of covariates for association with a response variable") + (description + "The global test tests groups of covariates (or features) for association +with a response variable. This package implements the test with diagnostic +plots and multiple testing utilities, along with several functions to +facilitate the use of this test for gene set testing of GO and KEGG terms.") + (license license:gpl2+))) + (define-public r-gostats (package (name "r-gostats") @@ -7475,13 +7907,13 @@ previously been used in XCMS.") (define-public r-numbat (package (name "r-numbat") - (version "1.2.2") + (version "1.3.0") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 - "06qq7i8k1mi7yg1irfbk3d2fmk7awvzj7h7r54hnr6pzywk7nmhc")))) + "0499i20kkpr58b59xmw7d4q4dgp6ryfb9jj55idvhaa2k1kv28n6")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape @@ -7962,14 +8394,14 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) + "14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) (propagated-inputs @@ -8368,6 +8800,33 @@ sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.") (license license:gpl3+))) +(define-public r-shinymethyl + (package + (name "r-shinymethyl") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "shinyMethyl" version)) + (sha256 + (base32 + "1xbadc4xszcqh211r8z0wp417f17aczz834icli17mcsl996ln3a")))) + (properties `((upstream-name . "shinyMethyl"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-illuminahumanmethylation450kmanifest + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/shinyMethyl") + (synopsis "Interactive visualization for Illumina methylation arrays") + (description + "This package provides an interactive tool for visualizing Illumina +methylation array data. Both the 450k and EPIC array are supported.") + (license license:artistic2.0))) + (define-public r-shortread (package (name "r-shortread") @@ -14341,6 +14800,46 @@ gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) +(define-public r-flowai + (package + (name "r-flowai") + (version "1.28.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "flowAI" version)) + (sha256 + (base32 + "18zrlnjw89iglxhw65ys8x4r44pdzp5chrgwx7w44sh7yd8576g9")))) + (properties `((upstream-name . "flowAI"))) + (build-system r-build-system) + (propagated-inputs + (list r-changepoint + r-flowcore + r-ggplot2 + r-knitr + r-plyr + r-rcolorbrewer + r-reshape2 + r-rmarkdown + r-scales)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/flowAI") + (synopsis + "Automatic and interactive quality control for flow cytometry data") + (description + "This package is able to perform an automatic or interactive quality +control on FCS data acquired using flow cytometry instruments. By evaluating +three different properties: + +@enumerate +@item flow rate +@item signal acquisition, and +@item dynamic range, +@end enumerate + +the quality control enables the detection and removal of anomalies.") + (license license:gpl2+))) + (define-public r-flowutils (package (name "r-flowutils") @@ -14616,14 +15115,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.36.0") + (version "3.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq")))) + "1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -15730,14 +16229,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.7") + (version "1.28.9") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0iv5c5p0g4axhanc62mmk0c43qcwdsxzslxh5qdck0v1kb7bd1d9")))) + "1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -17930,14 +18429,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g")))) + "1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -19518,14 +20017,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh")))) + "0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs |