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author | Ludovic Courtès <ludo@gnu.org> | 2022-04-28 16:24:46 +0200 |
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committer | Ludovic Courtès <ludo@gnu.org> | 2022-04-28 16:24:46 +0200 |
commit | 284fa7264963acc5d114ef5d54c347126b1654ba (patch) | |
tree | 3e5360fcc81b6d0dce76a65aca60cf8528f2931f /gnu/packages/bioconductor.scm | |
parent | 12c9da35389dfba86ae0d863132a6b2c4374205a (diff) | |
parent | 882cacc1bb5be0df334dd7ce55b385a3a1678728 (diff) | |
download | guix-patches-284fa7264963acc5d114ef5d54c347126b1654ba.tar guix-patches-284fa7264963acc5d114ef5d54c347126b1654ba.tar.gz |
Merge branch 'master' into staging
Diffstat (limited to 'gnu/packages/bioconductor.scm')
-rw-r--r-- | gnu/packages/bioconductor.scm | 1115 |
1 files changed, 883 insertions, 232 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 55d397e5cf..a78903becc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> @@ -557,6 +557,32 @@ several related annotation packages.") from several related annotation packages.") (license license:artistic2.0))) +(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 + (package + (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") + (version "0.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "IlluminaHumanMethylation450kanno.ilmn12.hg19" + version 'annotation)) + (sha256 + (base32 + "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) + (properties + `((upstream-name + . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page + "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") + (synopsis "Annotation for Illumina's 450k methylation arrays") + (description + "This package provides manifests and annotation for Illumina's 450k array +data.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -775,6 +801,44 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-snplocs-hsapiens-dbsnp144-grch37 + (package + (name "r-snplocs-hsapiens-dbsnp144-grch37") + (version "0.99.20") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" + version 'annotation)) + (sha256 + (base32 + "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) + (build-system r-build-system) + ;; As this package provides little more than a very large data file it + ;; doesn't make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (propagated-inputs + (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)") + (description "This package provides SNP locations and alleles for Homo +sapiens extracted from NCBI dbSNP Build 144. The source data files used for +this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped +to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a +patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, +X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for +the mitochondrion chromosome. Therefore, the SNPs in this package can be +injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the +correct position but this injection will exclude chrM (i.e. nothing will be +injected in that sequence).") + (license license:artistic2.0))) + (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene (package (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene") @@ -1118,48 +1182,6 @@ All datasets are restricted to protein coding genes.") (description "This package contains data used by @code{AneuFinder}.") (license license:artistic2.0))) -(define-public r-aneufinder - (package - (name "r-aneufinder") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AneuFinder" version)) - (sha256 - (base32 - "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) - (build-system r-build-system) - (native-inputs - (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 -calling, plotting, export and analysis from whole-genome single cell -sequencing data.") - (license license:artistic2.0))) - (define-public r-arrmdata (package (name "r-arrmdata") @@ -1253,34 +1275,6 @@ single-cell data or deconvolution of bulk RNA-seq.") chromstaR package.") (license license:gpl3))) -(define-public r-chromvarmotifs - (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") - (revision "1")) - (package - (name "r-chromvarmotifs") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/GreenleafLab/chromVARmotifs") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) - (properties `((upstream-name . "chromVARmotifs"))) - (build-system r-build-system) - (propagated-inputs - `(("r-tfbstools" ,r-tfbstools))) - (home-page "https://github.com/GreenleafLab/chromVARmotifs") - (synopsis "Stores motif collections for use with motifmatchr or chromVAR") - (description - "This package stores motif collections as lists of @dfn{position -frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} -package for use in R with packages like @code{motifmatchr} or -@code{chromVAR}.") - (license license:expat)))) - (define-public r-copyhelper (package (name "r-copyhelper") @@ -1532,6 +1526,399 @@ TCGAbiolinksGUI package.") ;;; Packages +(define-public r-abarray + (package + (name "r-abarray") + (version "1.62.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ABarray" version)) + (sha256 + (base32 + "0yh7jmkwdg3kmm98ii0cxbla3s5bwy84fpg6xcpggsrriwzwfb5k")))) + (properties `((upstream-name . "ABarray"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-multtest)) + (home-page "https://bioconductor.org/packages/ABarray") + (synopsis + "Gene expression analysis for Applied Biosystems Genome Survey Microarray") + (description + "The package @code{ABarray} is designed to work with Applied Biosystems +whole genome microarray platform, as well as any other platform whose data can +be transformed into expression data matrix. Functions include data +preprocessing, filtering, control probe analysis, statistical analysis in one +single function. A @dfn{graphical user interface} (GUI) is also provided. The +raw data, processed data, graphics output and statistical results are organized +into folders according to the analysis settings used.") + (license license:gpl2+))) + +(define-public r-absseq + (package + (name "r-absseq") + (version "1.48.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ABSSeq" version)) + (sha256 + (base32 + "0l2hh6qv4lhw1g1kciw2f3ssj3lw83hqxnkmxzmv7snik3k6i650")))) + (properties `((upstream-name . "ABSSeq"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-locfit)) + (home-page "https://bioconductor.org/packages/ABSSeq") + (synopsis + "RNA-Seq analysis based on modelling absolute expression differences") + (description + "This package implements a new RNA-Seq analysis method and integrates two +modules: a basic model for pairwise comparison and a linear model for complex +design. RNA-Seq quantifies gene expression with reads count, which usually +consists of conditions (or treatments) and several replicates for each +condition. This software infers differential expression directly by the +counts difference between conditions. It assumes that the sum counts +difference between conditions follow a negative binomial distribution. In +addition, @code{ABSSeq} moderates the fold-changes by two steps: the +expression level and gene-specific dispersion, that might facilitate the gene +ranking by fold-change and visualization.") + (license license:gpl3+))) + +(define-public r-adam + (package + (name "r-adam") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAM" version)) + (sha256 + (base32 + "18zwci0ab54q7rdwj0n63w0i14lfrb4cccp09bcrq10gl1ki07f5")))) + (properties `((upstream-name . "ADAM"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-dt + r-go-db + r-keggrest + r-knitr + r-pbapply + r-rcpp + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAM") + (synopsis "Gene activity and diversity analysis module") + (description + "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) +package created to group a set of genes from comparative samples (control +versus experiment) belonging to different species according to their respective +functions. The corresponding roles are extracted from the default collections +like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG). +@code{ADAM} show their significance by calculating the p-values referring to +gene diversity and activity. Each group of genes is called @dfn{Group of +functionally associated genes} (GFAG).") + (license license:gpl2+))) + +(define-public r-adamgui + (package + (name "r-adamgui") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADAMgui" version)) + (sha256 + (base32 + "0n06bb9djigha0249lxx84pn9q0xiryxbv25qsc3p2h46iaxi3wq")))) + (properties `((upstream-name . "ADAMgui"))) + (build-system r-build-system) + (propagated-inputs + (list r-adam + r-colorramps + r-data-table + r-dplyr + r-dt + r-ggplot2 + r-ggpubr + r-ggrepel + r-ggsignif + r-go-db + r-gridextra + r-knitr + r-rcolorbrewer + r-reshape2 + r-shiny + r-shinyjs + r-stringi + r-stringr + r-testthat + r-varhandle)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADAMgui/") + (synopsis "GUI for gene activity and diversity analysis") + (description + "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI) +for the @code{ADAM} package. The @code{ADAMgui} package provides two +shiny-based applications that allows the user to study the output of the +@code{ADAM} package files through different plots. It's possible, for +example, to choose a specific @dfn{group of functionally associated +genes} (GFAG) and observe the gene expression behavior with the plots created +with the @code{GFAGtargetUi} function. Features such as differential +expression and fold change can be easily seen with aid of the plots made with +the @code{GFAGpathUi} function.") + (license license:gpl2+))) + +(define-public r-adimpute + (package + (name "r-adimpute") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ADImpute" version)) + (sha256 + (base32 + "1bkq1hd8sqg9r28r70a9vd3gb2nsmg6dybf002d621p88cdfjib2")))) + (properties `((upstream-name . "ADImpute"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-checkmate + r-data-table + r-drimpute + r-kernlab + r-mass + r-matrix + r-rsvd + r-s4vectors + r-saver + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ADImpute") + (synopsis "Adaptive computational prediction for dropout imputations") + (description + "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically +unable to quantify the expression levels of all genes in a cell, creating a +need for the computational prediction of missing values (dropout imputation). +Most existing dropout imputation methods are limited in the sense that they +exclusively use the scRNA-seq dataset at hand and do not exploit external +gene-gene relationship information. The @code{ADImpute} package proposes two +methods to address this issue: + +@enumerate +@item a gene regulatory network-based approach using gene-gene relationships + learnt from external data; +@item a baseline approach corresponding to a sample-wide average. +@end enumerate + +@code{ADImpute} implements these novel methods and also combines them with +existing imputation methods like @code{DrImpute} and @code{SAVER}. +@code{ADImpute} can learn the best performing method per gene and combine the +results from different methods into an ensemble.") + (license license:gpl3+))) + +(define-public r-adsplit + (package + (name "r-adsplit") + (version "1.64.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "adSplit" version)) + (sha256 + (base32 + "1b4ck371h3a76m5h0brvlzsyg1g6q5fjrhra5hqv9pwxr330h9r2")))) + (properties `((upstream-name . "adSplit"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biobase + r-cluster + r-go-db + r-keggrest + r-multtest)) + (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml") + (synopsis "Annotation-driven splits in microarray data") + (description + "This package implements clustering of microarray gene expression +profiles according to functional annotations. For each term genes are +annotated to, splits into two subclasses are computed and a significance of +the supporting gene set is determined.") + (license license:gpl2+))) + +(define-public r-affixcan + (package + (name "r-affixcan") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AffiXcan" version)) + (sha256 + (base32 + "06yn87briv2141jqad934gg5rcd90w5nghrgmbhqnmwafn72gj9d")))) + (properties `((upstream-name . "AffiXcan"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-crayon + r-multiassayexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AffiXcan") + (synopsis "Functional approach to impute genetically regulated expression") + (description + "The @code{AffiXcan} package imputes a @dfn{genetically regulated +expression} (GReX) for a set of genes in a sample of individuals, using a +method based on the @dfn{total binding affinity} (TBA). Statistical models to +impute GReX can be trained with a training dataset where the real total +expression values are known.") + (license license:gpl3))) + +(define-public r-affyrnadegradation + (package + (name "r-affyrnadegradation") + (version "1.40.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AffyRNADegradation" version)) + (sha256 + (base32 + "00hzr62xn1i1w4g8krsxhivzwn8hd7hwhkdxyrpz6cs9vgr4x9kd")))) + (properties `((upstream-name . "AffyRNADegradation"))) + (build-system r-build-system) + (propagated-inputs (list r-affy)) + (home-page "https://bioconductor.org/packages/AffyRNADegradation") + (synopsis + "Analyze and correct probe positional bias in data due to RNA degradation") + (description + "The @code{AffyRNADegradation} package helps with the assessment and +correction of RNA degradation effects in Affymetrix 3 expression arrays. The +parameter @code{d} gives a robust and accurate measure of RNA integrity. The +correction removes the probe positional bias, and thus improves comparability +of samples that are affected by RNA degradation.") + ;; the R file header specifies GPL2 or later + (license license:gpl2+))) + +(define-public r-agdex + (package + (name "r-agdex") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AGDEX" version)) + (sha256 + (base32 + "0y0q4zdybr5hlsi7qy2hf6c2sqr2z2211wz36dz70jkqyr0ggw64")))) + (properties `((upstream-name . "AGDEX"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-gseabase)) + (home-page "https://bioconductor.org/packages/AGDEX") + (synopsis + "Evaluate agreement of differential expression for cross-species genomics") + (description + "The objective of @code{AGDEX} is to evaluate whether the results of a +pair of two-group differential expression analysis comparisons show a level of +agreement that is greater than expected if the group labels for each two-group +comparison are randomly assigned. The agreement is evaluated for the entire +transcriptome and (optionally) for a collection of pre-defined gene-sets. +Additionally, the procedure performs permutation-based differential expression +and meta analysis at both gene and gene-set levels of the data from each +experiment.") + (license license:gpl2+))) + +(define-public r-aggregatebiovar + (package + (name "r-aggregatebiovar") + (version "1.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "aggregateBioVar" version)) + (sha256 + (base32 + "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk")))) + (properties `((upstream-name . "aggregateBioVar"))) + (build-system r-build-system) + (propagated-inputs + (list r-matrix + r-rlang + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/jasonratcliff/aggregateBioVar") + (synopsis "Differential gene expression analysis for multi-subject scRNA-seq") + (description + "This package @code{aggregateBioVar} contains tools to summarize single +cell gene expression profiles at the level of subject for single cell RNA-seq +data collected from more than one subject (e.g. biological sample or technical +replicates). A @code{SingleCellExperiment} object is taken as input and +converted to a list of @code{SummarizedExperiment} objects, where each list +element corresponds to an assigned cell type. The @code{SummarizedExperiment} +objects contain aggregate gene-by-subject count matrices and inter-subject +column metadata for individual subjects that can be processed using downstream +bulk RNA-seq tools.") + (license license:gpl3))) + +(define-public r-agilp + (package + (name "r-agilp") + (version "3.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "agilp" version)) + (sha256 + (base32 + "02cyc2y4v3y16zlrnax2c96b2qfxj6b2j37ps4g2gdqgas08n9xp")))) + (properties `((upstream-name . "agilp"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/agilp") + (synopsis "Processing of Agilent expression array") + (description + "This package aims to provide a pipeline for the low-level analysis of +gene expression microarray data, primarily focused on the Agilent platform, +but which also provides utilities which may be useful for other platforms.") + ;; Some files are under GPLv2+ but the combined work is released under the + ;; GPLv3. + (license license:gpl3))) + +(define-public r-aneufinder + (package + (name "r-aneufinder") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AneuFinder" version)) + (sha256 + (base32 + "0xn8952fkchhx7m8dam6gjy86j551xp1cs67510s1qrmfgzpkjp0")))) + (build-system r-build-system) + (native-inputs + (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 +calling, plotting, export and analysis from whole-genome single cell +sequencing data.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") @@ -2052,14 +2439,14 @@ mapping.") (define-public r-nmf (package (name "r-nmf") - (version "0.23.0") + (version "0.24.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 - "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) + "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs @@ -2402,14 +2789,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.2.0") + (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0ks8yzvvs2r66pb9687mkskf0n3wgvp7h92k83b0a1q32sca5wng")))) + "08dk4h07gpi3rk9s80wrbx2ww2chj688qzbwlx8n4dz788lqbfz8")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -2519,13 +2906,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.50.1") + (version "2.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz")))) + "01mv05fj5iqvjb5xz9k92kx1a9d95mprb6isy57n0x20vd3cxdx1")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -3137,14 +3524,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.18.2") + (version "2.18.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0q56gv0isa9ayw505py7i7x65pvcshmd2j1mna1wpbk66wqj4qzx")))) + "1nsdcsghhh3ikv0hbn1aazdam7a6pqf1p6rz68ll2h6965kl4qzp")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -3327,13 +3714,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1r0wblz9w4hqxm15wdssz0invx7hxhg3bnblkia6w3aazh30s6ns")))) + "1ly851w6xy144qvmpdv7p64yc45bqxmvny2rzgz691h3qbin3x55")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -3387,13 +3774,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.46.3") + (version "1.46.5") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0a3shdzc1r0f12q9w679hgj8ywrwbg36z7k0yp47dgfjl14lachk")))) + "1fhahqh87cikfrwqkm2z4nq3jyi530qvsbmf09j2hyhsm87hhrgg")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -3667,16 +4054,37 @@ Shiny-based display methods for Bioconductor objects.") @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.") (license license:artistic2.0))) +(define-public r-lfa + (package + (name "r-lfa") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "lfa" version)) + (sha256 + (base32 "02b90xjb2lfm86hbsdrvzpv20pijnq78ibz4dwjzqd9v4xhia3wr")))) + (properties `((upstream-name . "lfa"))) + (build-system r-build-system) + (propagated-inputs (list r-corpcor)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/StoreyLab/lfa") + (synopsis "Logistic Factor Analysis for categorical data") + (description + "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on +Binomial data via estimation of latent structure in the natural parameter.") + (license license:gpl3))) + (define-public r-limma (package (name "r-limma") - (version "3.50.0") + (version "3.50.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "05ypmax1s6y1nz42bxn61wxhzzw6185q633crzpdcbbz3dz4vgvy")))) + "1p46sif1aygmw2p8ifiylxrrbfbgvcsa0zp40nxlxawc7h56rybp")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3763,14 +4171,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.4.0") + (version "3.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1n9rakj57yf17hay1bzvwc2h761yijmlflb3crg1bzwvmn32yhsl")))) + "0i6fq6736gvrqn45r7nrhl0ns45qwj1bl4yc6qlalw2g46mjxf6k")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3809,14 +4217,14 @@ in SNV base substitution data.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.20.1") + (version "2.20.4") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0ip614mdwisz2hlmyfgngysq1s3hajb88cgdmygfc8i6kyxjkjzl")))) + "0d3b0i154dyz1wvy2jwf5831bzbmalw7rzvxj8rd7658zjhghgzc")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -4150,14 +4558,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "0y1mawzfvxrympc47q3isk96sl9d1bc8kdsxpm8rnhqg5bmgwya6")))) + "0k500fdmv5l0v7b9pj73bjk3h9k261mfqi6vl52khlw0fafn9b6p")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -4231,13 +4639,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.38.0") + (version "2.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "13zm993l3i9f98gqdpxgsrzf9fgqppx2ajvrl0i3f7cvpifcgxqg")))) + "1mlwp7bblhbpmd90sxj02zpq1q3fyg8v7ankyjb1y284xaymp02y")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) @@ -4710,13 +5118,13 @@ structures to hold pseudotime inference results.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "081kp9b0lpw2xq9xvd2kykqqrqcj322mp7xa44xc3kf0nzsivqfa")))) + "10kjpmckhzjf41yfhzg7c8idqa9cxz33r4rza6rwihnqnw1liff3")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -4739,16 +5147,39 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +(define-public r-stager + (package + (name "r-stager") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "stageR" version)) + (sha256 + (base32 "0vpx0v04hgkhzi0bm7ipnb9xr37n5wvnnr45lljgni8pwabfkf6y")))) + (properties `((upstream-name . "stageR"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/stageR") + (synopsis "Stage-wise analysis of high throughput gene expression data") + (description + "The stageR package allows automated stage-wise analysis of +high-throughput gene expression data. The method is published in Genome +Biology at +@url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.") + (license license:gpl3))) + (define-public r-stringdb (package (name "r-stringdb") - (version "2.6.0") + (version "2.6.5") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm")))) + (base32 "0n2r2zc2sx1a2a8wqqxz6z7i4ynaj18iwbwgif7469n13agji5mv")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -4877,14 +5308,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.0.5") + (version "2.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "1j91pyfjsqngxxlxjqc477pznlfax4vayrks2q12rxw76ija80hf")))) + "0ajlw9yg6fha76rkkmsk5niq99s33k9437bkgi9whgh3pa6bkab2")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -5077,6 +5508,43 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) +;; There is no source tarball, so we fetch the code from the Bioconductor git +;; repository. +(define-public r-xcir + (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277") + (revision "1")) + (package + (name "r-xcir") + (version (git-version "1.8.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://git.bioconductor.org/packages/XCIR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p")))) + (properties `((upstream-name . "XCIR"))) + (build-system r-build-system) + (propagated-inputs (list r-biomart + r-biostrings + r-data-table + r-ggplot2 + r-iranges + r-readxl + r-s4vectors + r-seqminer + r-variantannotation)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/SRenan/XCIR") + (synopsis "Analysis of X chromosome inactivation") + (description + "This package is an R package that offers models and tools for subject +level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape +inference.") + (license license:gpl2)))) + (define-public r-xina (package (name "r-xina") @@ -5432,14 +5900,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.4.3") + (version "3.4.11") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1bz03ls7pkb09p6nkz7gfnhjlh06mgbp3j98ppnzibiar3cjrnfj")))) + "1xprj3x3s3yh6fwsdcl4zgfbhn640422x1lhhrmvdr836jr8sxcj")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -5670,14 +6138,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.28.0") + (version "3.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "05fbq8zvww1nlyykrri0hf4248i1i7w5cr453giagmjq7lgg4v3b")))) + "0v2qz3rp5lmj3s1ziahjqym6cjlh4wdvf050k1x6dx8404jhi8kw")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -6453,14 +6921,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.8.0") + (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "01662p5j9l12ylf5a5djg4cjppd2n3chrygzw8nnrcf1806xn58y")))) + "1f2mp2sxbf1zi61npj5rl5pl7z30rkj5953521iiv0w99mdfwhsc")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -6486,7 +6954,7 @@ possible, parallelization is achieved using the BiocParallel framework.") r-tidyselect r-vim)) (native-inputs - (list r-nbconvertr)) ; for vignettes + (list r-knitr 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 @@ -6699,13 +7167,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.20.0") + (version "1.20.3") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "0x3mld9q55r2fy452wxq5sjzmms10zmpkzs71c3w1fdli5hwszdq")))) + "0bcc1ln7602lrbm9wckgyfd9slsqiljjmymj28rfpax1n8rbq44m")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -7231,14 +7699,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.62.1") + (version "2.62.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0plmh4x37r848g6ilvl1x8cim90rp85gikfc5m8lgi2i4xkq7hbq")))) + "1hncr0p54qdg82a771yjjm4w1k2myrc26jzvci3g37mq7bgv3mxw")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -7947,14 +8415,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0nsx96mkcg0hhg3x8jndzq3xvq9bq7m4yf1b3ry73b17ladx81ch")))) + "1rjiqmc32c9gxckgrgbypxpp0m8y0kahvhzvjzymda25xp8zqjs2")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -7985,14 +8453,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.2.1") + (version "4.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "08jhcbanz24x7zdkxznxz787g0nk3jfzd7zsap13sra7qnwaswq4")))) + "1y8ay3fxvcc7a7yqvfc95jfn800ikvs56j17byyp6v08w2j00y76")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -8528,14 +8996,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "18fzi2qi95851ci7qrzwpb7v6fhwp6xi1d1vk11xbygpbvql5mls")))) + "17v2v7aklljy17nivwmani2jxkbffqs2yr38hlspjlvgpidpf9ln")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -8565,14 +9033,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "0i1i3bfkp1xsjdl1nd56mlh66qz3aasd1hp09d4i31njz2f9znwn")))) + "1jmlialnhs9df1hv6l4qk2c4qjyjbz9mdj8vr52ms8vlxlxplz6c")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -9230,14 +9698,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.60.0") + (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "1icqyxkx5a9y3wahkxpxngw85c7l4hih1ym9nwwn9qy93pnw1zi4")))) + "00irq3i5kfck7rnm8ll7rqhqfpp3bisv2h8is50a7wbd7480z7ij")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -9292,6 +9760,47 @@ imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.") (license license:gpl2+))) +(define-public r-wppi + (package + (name "r-wppi") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "wppi" version)) + (sha256 + (base32 + "1spwa8p6w3pyw21dvd1lrhcz1sphdsmsd408jv55ss9nbgvgrp23")))) + (properties `((upstream-name . "wppi"))) + (build-system r-build-system) + ;; This is necessary because omnipathr attempts to write a configuration + ;; file to HOME. + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs (list r-dplyr + r-igraph + r-logger + r-magrittr + r-matrix + r-omnipathr + r-progress + r-purrr + r-rcurl + r-rlang + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/AnaGalhoz37/wppi") + (synopsis "Weighting protein-protein interactions") + (description + "This package predicts functional relevance of protein-protein +interactions based on functional annotations such as Human Protein Ontology +and Gene Ontology, and prioritizes genes based on network topology, functional +scores and a path search algorithm.") + (license license:expat))) + (define-public r-wrench (package (name "r-wrench") @@ -9544,14 +10053,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "11qayqmgv274hc4h1v222sma07wkxjm8002fl6w3yvi225zq1qc1")))) + "0gaj0z6dk2p2vhvqz685xwd5q2mkvpimh2493p3w04s2rlsvi3jb")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -9617,6 +10126,18 @@ Gaussian distributions.") "0ardmryx6ac7v6n900a1klrrldvbmh7bxvy8ldz8rwid19h29ikr")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) + (arguments + `(#:phases + ;; Disable unsupported `popcnt' instructions on + ;; architectures other than x86_64 + ,(if (string-prefix? "x86_64" + (or (%current-target-system) + (%current-system))) + '%standard-phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-sources + (lambda _ + (setenv "POPCNT_CAPABILITY" "0"))))))) (inputs (list zlib)) (native-inputs (list r-knitr)) @@ -9797,18 +10318,18 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.26.0") + (version "3.26.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0ki4rcwjgbixzy5q9s30ajx5zhpl18q50znrb60fchvl4hj9h93w")))) + "041i5d08bsc5jqx3309fixjacizs4yi992cwazxghm8mrk3kicbr")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs - (list r-igraph r-matrix r-slam r-tsne)) + (list r-igraph r-matrix r-rtsne r-slam)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description @@ -9887,14 +10408,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "0mz5lrdsihx66sgx9klnvpxvw1mjjcbijcsdbgxwaimzl9k1kr05")))) + "19f3wd55860x959h5n7mrivyjdas5b3jmx74lf24xnx23g26f8rn")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multidataset)) @@ -9994,14 +10515,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.8.1") + (version "2.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0lpx0dp5570kbrq7v0g573axkhi00qrf38si59vmvnqxhmkvsixn")))) + "078zcchw9xl6vs2wihzzji349vq0m1a039m86jdlvb7nc3i1imfk")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -10066,17 +10587,60 @@ and to both short and long sequence reads.") cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) +;; This is the latest commit and it solves a bug from the latest release. +(define-public r-cycombine + (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1")) + (package + (name "r-cycombine") + (version (git-version "0.2.6" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biosurf/cyCombine") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm")))) + (properties `((upstream-name . "cyCombine"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-cytolib + r-dplyr + r-flowcore + r-ggplot2 + r-knitr + r-kohonen + r-magrittr + r-purrr + r-rcolorbrewer + r-readr + r-readxl + r-stringr + r-sva + r-tibble + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/biosurf/cyCombine") + (synopsis "Integration of single-cell cytometry datasets") + (description + "This package provides a method for combining single-cell cytometry +datasets, which increases the analytical flexibility and the statistical power +of the analyses while minimizing technical noise.") + (license license:expat)))) + (define-public r-cytolib (package (name "r-cytolib") - (version "2.6.1") + (version "2.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "16m5w6cp28p4fs2p8c8rjcg1d686xl8mpas816i7zxfh8m0bcqc9")))) + "0ycr4wmkfi0rvzwicblkfjgppk72gwwpim0rfiz1s44lycsf4py5")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -10950,32 +11514,6 @@ regulatory networks from expression data.") Characteristic} (ROC) curves, with a focus on micro arrays.") (license license:artistic2.0))) -(define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 - (package - (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") - (version "0.6.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri - "IlluminaHumanMethylation450kanno.ilmn12.hg19" - version 'annotation)) - (sha256 - (base32 - "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) - (properties - `((upstream-name - . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) - (build-system r-build-system) - (propagated-inputs (list r-minfi)) - (home-page - "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") - (synopsis "Annotation for Illumina's 450k methylation arrays") - (description - "This package provides manifests and annotation for Illumina's 450k array -data.") - (license license:artistic2.0))) - (define-public r-watermelon (package (name "r-watermelon") @@ -11125,44 +11663,6 @@ and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) -(define-public r-snplocs-hsapiens-dbsnp144-grch37 - (package - (name "r-snplocs-hsapiens-dbsnp144-grch37") - (version "0.99.20") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" - version 'annotation)) - (sha256 - (base32 - "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - (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)") - (description "This package provides SNP locations and alleles for Homo -sapiens extracted from NCBI dbSNP Build 144. The source data files used for -this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped -to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a -patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, -X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for -the mitochondrion chromosome. Therefore, the SNPs in this package can be -injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the -correct position but this injection will exclude chrM (i.e. nothing will be -injected in that sequence).") - (license license:artistic2.0))) - (define-public r-reqon (package (name "r-reqon") @@ -11383,19 +11883,20 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "0f5y61dpzwmr8v7npim18zvxa8n49rbzclb9j72haba0px6ibhvw")))) + "14aki7d9xl4rhhzv3cl09mbj1q7xhxg69s4kzms9hfv3cqjryqd7")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) (propagated-inputs - (list r-biobase + (list r-aod + r-biobase r-biocparallel r-doparallel r-foreach @@ -11409,7 +11910,9 @@ arrays based on fast wavelet-based functional models.") r-matrix r-pbkrtest r-progress + r-rdpack r-reshape2 + r-rhpcblasctl r-rlang r-scales)) (native-inputs @@ -11482,14 +11985,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.12.2") + (version "1.12.4") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1p9zdrsxqn4ayvbj05xgpzpbzkzrh7k0d62x10069687vfl6dlxg")))) + "01skcvzd815m3c15ka2pk7z6bggc4l8bhvaf4z9v95i36k4mn5zd")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11527,6 +12030,111 @@ enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.") (license license:gpl3))) +(define-public r-ace + (package + (name "r-ace") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACE" version)) + (sha256 + (base32 + "1nkbxldn5ba4fzfh4skwjc37gm6apwp09vzwnj2jw3b7ivmr0yr6")))) + (properties `((upstream-name . "ACE"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tgac-vumc/ACE") + (synopsis + "Absolute copy number estimation from low-coverage whole genome sequencing") + (description + "This package uses segmented copy number data to estimate tumor cell +percentage and produce copy number plots displaying absolute copy numbers. For +this it uses segmented data from the @code{QDNAseq} package, which in turn uses +a number of dependencies to turn mapped reads into segmented data. @code{ACE} +will run @code{QDNAseq} or use its output rds-file of segmented data. It will +subsequently run through all samples in the object(s), for which it will create +individual subdirectories. For each sample, it will calculate how well the +segments fit (the relative error) to integer copy numbers for each percentage +of @dfn{tumor cells} (cells with divergent segments).") + (license license:gpl2))) + +(define-public r-acgh + (package + (name "r-acgh") + (version "1.72.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "aCGH" version)) + (sha256 + (base32 + "1r1q6iq3g7svfn5m4jxlxp413djb40mvf6lh595y86sgwav5k6l4")))) + (properties `((upstream-name . "aCGH"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) + (home-page "https://bioconductor.org/packages/aCGH") + (synopsis + "Classes and functions for array comparative genomic hybridization data") + (description + "This package provides functions for reading +@dfn{array comparative genomic hybridization} (aCGH) data from image analysis +output files and clone information files, creation of @code{aCGH} objects for +storing these data. Basic methods are accessing/replacing, subsetting, +printing and plotting @code{aCGH} objects.") + (license license:gpl2))) + +(define-public r-acme + (package + (name "r-acme") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ACME" version)) + (sha256 + (base32 + "0h4bqbbqcwc938q7lysk5l35f64xz9d1bsniv2wshmlr4rr0zpcg")))) + (properties `((upstream-name . "ACME"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-biocgenerics)) + (home-page "https://bioconductor.org/packages/aCGH/") + (synopsis "Calculating microarray enrichment") + (description + "This package implements @dfn{algorithms for calculating microarray +enrichment} (ACME), and it is a set of tools for analysing tiling array of +@dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip), +DNAse hypersensitivity, or other experiments that result in regions of the +genome showing enrichment. It does not rely on a specific array technology +(although the array should be a tiling array), is very general (can be applied +in experiments resulting in regions of enrichment), and is very insensitive to +array noise or normalization methods. It is also very fast and can be applied +on whole-genome tiling array experiments quite easily with enough memory.") + (license license:gpl2+))) + +(define-public r-acde + (package + (name "r-acde") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "acde" version)) + (sha256 + (base32 + "13ks87am73m3bjn9ljapxml2a9cxdpgv9flwvly8aqmi3ndxyqi6")))) + (properties `((upstream-name . "acde"))) + (build-system r-build-system) + (propagated-inputs (list r-boot)) + (home-page "https://bioconductor.org/packages/acde") + (synopsis + "Identification of differentially expressed genes with artificial components") + (description + "This package provides a multivariate inferential analysis method for +detecting differentially expressed genes in gene expression data. It uses +artificial components, close to the data's principal components but with an +exact interpretation in terms of differential genetic expression, to identify +differentially expressed genes while controlling the @dfn{false discovery +rate} (FDR).") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs @@ -12235,14 +12843,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "15las4qmqvrn81hczxa3ylikqh54kp1lg9r8rcyfvrx5l0kgwlfq")))) + "0lvd6hyqdfsn5ji714v46qdrb8vr1y38lv0pgw8priab0hpqrbm5")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -12791,13 +13399,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.32.3") + (version "0.32.4") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw")))) + "17dvypxcwp8c7ih23hi2366110by6zq1mjgxkmlbiklzachg9780")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -13315,13 +13923,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "19lsn3cpghkhfbx4jqgbwwrnacrl7vj3r91ymd1gk02c9pn5dmci")))) + (base32 "0j0h6ipm65wv38qx40z16h01mfirpshfn4lhlwlg2nri4vmihlpi")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -13527,14 +14135,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.6.0") + (version "1.6.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "1w8d1v2r3plwwcz23zhbpvklhapf2a6x3xmglyh4sh6sy9ynkgrv")))) + "0614a830gf676ck8j5lkm04158pfvhjb61p3xfdd69gg3d44mk1d")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -13671,14 +14279,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "15lah45lf16zh1ankbpjvz8zp38lldvq074nmvb99rhhqys2gbgi")))) + "0dvcs7nz1yawcrsf9lqiwdcrvjmbs8ajrmvj0ji4qq2a86n3dkg0")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13710,20 +14318,25 @@ relevant, and the minimum expression of the most abundant condition.") r-summarizedexperiment)) (native-inputs (list r-knitr)) - (home-page - "https://github.com/HelenaLC/CATALYST") + (home-page "https://github.com/HelenaLC/CATALYST") (synopsis "Cytometry data analysis tools") (description - "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass -cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as -reporters to label antibodies, thereby substantially decreasing spectral -overlap and allowing for examination of over 50 parameters at the single cell -level. While spectral overlap is significantly less pronounced in CyTOF than -flow cytometry, spillover due to detection sensitivity, isotopic impurities, -and oxide formation can impede data interpretability. We designed -CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for -preprocessing of cytometry data, including i) normalization using bead -standards, ii) single-cell deconvolution, and iii) bead-based compensation.") + "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass +cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal +isotopes rather than fluorescent tags as reporters to label antibodies, +thereby substantially decreasing spectral overlap and allowing for examination +of over 50 parameters at the single cell level. While spectral overlap is +significantly less pronounced in CyTOF than flow cytometry, spillover due to +detection sensitivity, isotopic impurities, and oxide formation can impede +data interpretability. @code{CATALYST} was designed to provide a pipeline for +preprocessing of cytometry data, including: + +@enumerate +@item normalization using bead standards; +@item single-cell deconvolution; +@item bead-based compensation. +@end enumerate +") (license license:gpl2+))) (define-public r-erma @@ -13937,14 +14550,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.38.0") + (version "1.38.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0nqa7m300d7gpsayb6c6rv64d3y8c390wvwgz7v29zs9c025s9a8")))) + "14qybi5b3h9z5b0m127jf7z695amf612rh5wq2g2n1yirfhzbdja")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -14106,20 +14719,21 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.6-0") + (version "2.7-0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "0fr5pyc43hly5ry5bbygibbh9mnql7vl4r5qz42d0ry4hahyxa4w")))) + "13i2f4lw1rzj89bp31sn03prq1bqj7bsxwdr8z2ql02yqks9phg0")))) (build-system r-build-system) (inputs (list gsl)) (propagated-inputs (list r-doparallel r-foreach + r-graph r-lme4 r-nnet r-rcpp @@ -14452,14 +15066,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.20.0") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "0pjymal01sjl5dc37g66wykgxnksarlbvwnbvhg7w0i7y92zavqk")))) + "0mrw7fwjx8k0a5c3iw2j94h1yn5pkvqil7fbzih9xiafnpbn374m")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -15153,13 +15767,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.2.0") + (version "3.2.8") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "1q89mxnp8cig9r1499g7fb9p9x9ryz1dmc3w6ps5ww9n6rl8jqk8")))) + (base32 "0vr16ar3rbjsfw4qz2g86lbhvmqwgq0vcahc6vrc4d9rdjxwg6sb")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -15256,13 +15870,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.22.2") + (version "2.22.4") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0l7hfwgd8aiqv2k98jchkr3sdp9hwdg7pzm3bnvr6k7p93ifr6wc")))) + (base32 "071wz6dm6dypbfzvxd6j67l1iawlb6d5sfzq871zh06fzaxjm332")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs @@ -15308,6 +15922,43 @@ regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.") (license license:gpl3+))) +(define-public r-tricycle + (package + (name "r-tricycle") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tricycle" version)) + (sha256 + (base32 + "19yh7yif8630j845m9rddva2z0xy4jcw9j4hvyr076jqbyxz998r")))) + (properties `((upstream-name . "tricycle"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-circular + r-dplyr + r-genomicranges + r-ggplot2 + r-iranges + r-rcolorbrewer + r-s4vectors + r-scater + r-scattermore + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hansenlab/tricycle") + (synopsis "Transferable representation and inference of cell cycle") + (description + "The package contains functions to infer and visualize cell cycle process +using Single-cell RNA-Seq data. It exploits the idea of transfer learning, +projecting new data to the previous learned biologically interpretable space. +The @code{tricycle} provides a pre-learned cell cycle space, which could be +used to infer cell cycle time of human and mouse single cell samples. In +addition, it also offer functions to visualize cell cycle time on different +embeddings and functions to build new reference.") + (license license:gpl3))) + (define-public r-tximeta (package (name "r-tximeta") |