diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 1464 |
1 files changed, 1413 insertions, 51 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 8fe56c4a5b..88dca552e0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,11 +1,15 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> +;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> +;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> +;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> -;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> +;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -389,6 +393,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-genomeinfodbdata + (package + (name "r-genomeinfodbdata") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) + (sha256 + (base32 + "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) + (properties + `((upstream-name . "GenomeInfoDbData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/GenomeInfoDbData") + (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") + (description "This package contains data for mapping between NCBI taxonomy +ID and species. It is used by functions in the GenomeInfoDb package.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") @@ -905,6 +928,26 @@ All datasets are restricted to protein coding genes.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-chromstardata + (package + (name "r-chromstardata") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chromstaRData" version 'experiment)) + (sha256 + (base32 + "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab")))) + (properties `((upstream-name . "chromstaRData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/chromstaRData/") + (synopsis "ChIP-seq data for demonstration purposes") + (description + "This package provides ChIP-seq data for demonstration purposes in the +chromstaR package.") + (license license:gpl3))) + (define-public r-genelendatabase (package (name "r-genelendatabase") @@ -1190,6 +1233,39 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-delayedarray + (package + (name "r-delayedarray") + (version "0.16.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedArray" version)) + (sha256 + (base32 + "0w1wppy6m2iv41852dscg3y19sq84ahdx3m7c2p2pxjcznmv6hys")))) + (properties + `((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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DelayedArray") + (synopsis "Delayed operations on array-like objects") + (description + "Wrapping an array-like object (typically an on-disk object) in a +@code{DelayedArray} object allows one to perform common array operations on it +without loading the object in memory. In order to reduce memory usage and +optimize performance, operations on the object are either delayed or executed +using a block processing mechanism. Note that this also works on in-memory +array-like objects like @code{DataFrame} objects (typically with Rle columns), +@code{Matrix} objects, and ordinary arrays and data frames.") + (license license:artistic2.0))) + (define-public r-bluster (package (name "r-bluster") @@ -1243,6 +1319,89 @@ and evaluate clustering results.") arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-iranges + (package + (name "r-iranges") + (version "2.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IRanges" version)) + (sha256 + (base32 + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + (properties + `((upstream-name . "IRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/IRanges") + (synopsis "Infrastructure for manipulating intervals on sequences") + (description + "This package provides efficient low-level and highly reusable S4 classes +for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more +generally, data that can be organized sequentially (formally defined as +@code{Vector} objects), as well as views on these @code{Vector} objects. +Efficient list-like classes are also provided for storing big collections of +instances of the basic classes. All classes in the package use consistent +naming and share the same rich and consistent \"Vector API\" as much as +possible.") + (license license:artistic2.0))) + +;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. +(define-public r-absfiltergsea + (package + (name "r-absfiltergsea") + (version "1.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "AbsFilterGSEA" version)) + (sha256 + (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) + (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))) + (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") + (synopsis "Improved false positive control of gene-permuting with absolute filtering") + (description + "This package provides a function that performs gene-permuting of a gene-set +enrichment analysis (GSEA) calculation with or without the absolute filtering. + Without filtering, users can perform (original) two-tailed or one-tailed +absolute GSEA.") + (license license:gpl2))) + +;; This is a CRAN package, but it depends on r-biobase from Bioconductor. +(define-public r-bisquerna + (package + (name "r-bisquerna") + (version "1.0.4") + (source (origin + (method url-fetch) + (uri (cran-uri "BisqueRNA" version)) + (sha256 + (base32 + "01g34n87ml7n3pck77497ddgbv3rr5p4153ac8ninpgjijlm3jw2")))) + (properties `((upstream-name . "BisqueRNA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-limsolve" ,r-limsolve))) + (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 +abundances from heterogeneous bulk expression. A reference-based method +utilizes single-cell information to generate a signature matrix and +transformation of bulk expression for accurate regression based estimates. +A marker-based method utilizes known cell-specific marker genes to measure +relative abundances across samples.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs @@ -1487,6 +1646,500 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-annotationdbi + (package + (name "r-annotationdbi") + (version "1.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationDbi" version)) + (sha256 + (base32 + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + (properties + `((upstream-name . "AnnotationDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationDbi") + (synopsis "Annotation database interface") + (description + "This package provides user interface and database connection code for +annotation data packages using SQLite data storage.") + (license license:artistic2.0))) + +(define-public r-annotationforge + (package + (name "r-annotationforge") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationForge" version)) + (sha256 + (base32 + "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) + (properties + `((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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationForge") + (synopsis "Code for building annotation database packages") + (description + "This package provides code for generating Annotation packages and their +databases. Packages produced are intended to be used with AnnotationDbi.") + (license license:artistic2.0))) + +(define-public r-biobase + (package + (name "r-biobase") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biobase" version)) + (sha256 + (base32 + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + (properties + `((upstream-name . "Biobase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/Biobase") + (synopsis "Base functions for Bioconductor") + (description + "This package provides functions that are needed by many other packages +on Bioconductor or which replace R functions.") + (license license:artistic2.0))) + +(define-public r-biomart + (package + (name "r-biomart") + (version "2.46.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-progress" ,r-progress) + ("r-rappdirs" ,r-rappdirs) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + +(define-public r-biocparallel + (package + (name "r-biocparallel") + (version "1.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocParallel" version)) + (sha256 + (base32 + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + (properties + `((upstream-name . "BiocParallel"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + ;; Remove generated documentation. + (for-each delete-file + '("inst/doc/BiocParallel_BatchtoolsParam.pdf" + "inst/doc/Introduction_To_BiocParallel.pdf" + "inst/doc/Errors_Logs_And_Debugging.pdf" + "inst/doc/BiocParallel_BatchtoolsParam.R" + "inst/doc/Introduction_To_BiocParallel.R" + "inst/doc/Errors_Logs_And_Debugging.R")) + + ;; Remove time-dependent macro + (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" + "inst/doc/Introduction_To_BiocParallel.Rnw" + "inst/doc/Errors_Logs_And_Debugging.Rnw" + "vignettes/BiocParallel_BatchtoolsParam.Rnw" + "vignettes/Introduction_To_BiocParallel.Rnw" + "vignettes/Errors_Logs_And_Debugging.Rnw") + (("\\today") "later")) + + ;; Initialize the random number generator seed when building. + (substitute* "R/internal_rng_stream.R" + (("\"L'Ecuyer-CMRG\"\\)" m) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocParallel") + (synopsis "Bioconductor facilities for parallel evaluation") + (description + "This package provides modified versions and novel implementation of +functions for parallel evaluation, tailored to use with Bioconductor +objects.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-biostrings + (package + (name "r-biostrings") + (version "2.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biostrings" version)) + (sha256 + (base32 + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + (properties + `((upstream-name . "Biostrings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/Biostrings") + (synopsis "String objects and algorithms for biological sequences") + (description + "This package provides memory efficient string containers, string +matching algorithms, and other utilities, for fast manipulation of large +biological sequences or sets of sequences.") + (license license:artistic2.0))) + +(define-public r-category + (package + (name "r-category") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Category" version)) + (sha256 + (base32 + "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) + (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))) + (home-page "https://bioconductor.org/packages/Category") + (synopsis "Category analysis") + (description + "This package provides a collection of tools for performing category +analysis.") + (license license:artistic2.0))) + +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.30.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19")))) + (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))) + (home-page "https://bioconductor.org/packages/DESeq2") + (synopsis "Differential gene expression analysis") + (description + "This package provides functions to estimate variance-mean dependence in +count data from high-throughput nucleotide sequencing assays and test for +differential expression based on a model using the negative binomial +distribution.") + (license license:lgpl3+))) + +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + (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))) + (home-page "https://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + +(define-public r-edger + (package + (name "r-edger") + (version "3.32.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "edgeR" version)) + (sha256 + (base32 + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + (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 + (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 +RNA-seq expression profiles with biological replication. It implements a range +of statistical methodology based on the negative binomial distributions, +including empirical Bayes estimation, exact tests, generalized linear models +and quasi-likelihood tests. It be applied to differential signal analysis of +other types of genomic data that produce counts, including ChIP-seq, SAGE and +CAGE.") + (license license:gpl2+))) + +(define-public r-genefilter + (package + (name "r-genefilter") + (version "1.72.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genefilter" version)) + (sha256 + (base32 + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-survival" ,r-survival))) + (home-page "https://bioconductor.org/packages/genefilter") + (synopsis "Filter genes from high-throughput experiments") + (description + "This package provides basic functions for filtering genes from +high-throughput sequencing experiments.") + (license license:artistic2.0))) + +(define-public r-genomeinfodb + (package + (name "r-genomeinfodb") + (version "1.26.6") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDb" version)) + (sha256 + (base32 + "1wy4dwiv0pgim975var802z565py4a0nakx6zdvbhry4c0dfczd1")))) + (properties + `((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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomeInfoDb") + (synopsis "Utilities for manipulating chromosome identifiers") + (description + "This package contains data and functions that define and allow +translation between different chromosome sequence naming conventions (e.g., +\"chr1\" versus \"1\"), including a function that attempts to place sequence +names in their natural, rather than lexicographic, order.") + (license license:artistic2.0))) + +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + (properties + `((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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + +(define-public r-gostats + (package + (name "r-gostats") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOstats" version)) + (sha256 + (base32 + "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) + (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))) + (home-page "https://bioconductor.org/packages/GOstats") + (synopsis "Tools for manipulating GO and microarrays") + (description + "This package provides a set of tools for interacting with GO and +microarray data. A variety of basic manipulation tools for graphs, hypothesis +testing and other simple calculations.") + (license license:artistic2.0))) + +(define-public r-gseabase + (package + (name "r-gseabase") + (version "1.52.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GSEABase" version)) + (sha256 + (base32 + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GSEABase") + (synopsis "Gene set enrichment data structures and methods") + (description + "This package provides classes and methods to support @dfn{Gene Set +Enrichment Analysis} (GSEA).") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") @@ -1507,6 +2160,48 @@ microarrays.") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-limma + (package + (name "r-limma") + (version "3.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "limma" version)) + (sha256 + (base32 + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + (build-system r-build-system) + (home-page "http://bioinf.wehi.edu.au/limma") + (synopsis "Package for linear models for microarray and RNA-seq data") + (description "This package can be used for the analysis of gene expression +studies, especially the use of linear models for analysing designed experiments +and the assessment of differential expression. The analysis methods apply to +different technologies, including microarrays, RNA-seq, and quantitative PCR.") + (license license:gpl2+))) + +(define-public r-rbgl + (package + (name "r-rbgl") + (version "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RBGL" version)) + (sha256 + (base32 + "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) + (properties `((upstream-name . "RBGL"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bh" ,r-bh) + ("r-graph" ,r-graph))) + (home-page "https://www.bioconductor.org/packages/RBGL") + (synopsis "Interface to the Boost graph library") + (description + "This package provides a fairly extensive and comprehensive interface to +the graph algorithms contained in the Boost library.") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") @@ -1541,14 +2236,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.30.0") + (version "2.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31")))) + "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -1588,6 +2283,220 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (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))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (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))) + (home-page "https://bioconductor.org/packages/ShortRead") + (synopsis "FASTQ input and manipulation tools") + (description + "This package implements sampling, iteration, and input of FASTQ files. +It includes functions for filtering and trimming reads, and for generating a +quality assessment report. Data are represented as +@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of +purposes. The package also contains legacy support for early single-end, +ungapped alignment formats.") + (license license:artistic2.0))) + +(define-public r-systempiper + (package + (name "r-systempiper") + (version "1.24.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-assertthat" ,r-assertthat) + ("r-batchtools" ,r-batchtools) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) + ("r-edger" ,r-edger) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gostats" ,r-gostats) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) + ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-yaml" ,r-yaml) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tgirke/systemPipeR") + (synopsis "Next generation sequencing workflow and reporting environment") + (description + "This R package provides tools for building and running automated +end-to-end analysis workflows for a wide range of @dfn{next generation +sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. +Important features include a uniform workflow interface across different NGS +applications, automated report generation, and support for running both R and +command-line software, such as NGS aligners or peak/variant callers, on local +computers or compute clusters. Efficient handling of complex sample sets and +experimental designs is facilitated by a consistently implemented sample +annotation infrastructure.") + (license license:artistic2.0))) + +(define-public r-variantannotation + (package + (name "r-variantannotation") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "VariantAnnotation" version)) + (sha256 + (base32 + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + (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))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/VariantAnnotation") + (synopsis "Package for annotation of genetic variants") + (description "This R package can annotate variants, compute amino acid +coding changes and predict coding outcomes.") + (license license:artistic2.0))) + +(define-public r-xvector + (package + (name "r-xvector") + (version "0.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "XVector" version)) + (sha256 + (base32 + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + (properties + `((upstream-name . "XVector"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/XVector") + (synopsis "Representation and manpulation of external sequences") + (description + "This package provides memory efficient S4 classes for storing sequences +\"externally\" (behind an R external pointer, or on disk).") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") @@ -1796,14 +2705,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.13") + (version "3.0.15") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn")))) + "06f613s8d9z51njyf839g22gwybx9zs5n6xghwr5j1ad2n4m6qwi")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -2010,14 +2919,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.24.1") + (version "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) + "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -2026,6 +2935,7 @@ determining dependencies between variables, code improvement suggestions.") ("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) @@ -3688,33 +4598,6 @@ visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) -;; This is a CRAN package, but it depends on packages from Bioconductor. -(define-public r-gkmsvm - (package - (name "r-gkmsvm") - (version "0.81.0") - (source - (origin - (method url-fetch) - (uri (cran-uri "gkmSVM" version)) - (sha256 - (base32 - "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) - (properties `((upstream-name . "gkmSVM"))) - (build-system r-build-system) - (propagated-inputs - `(("r-kernlab" ,r-kernlab) - ("r-rcpp" ,r-rcpp) - ("r-rocr" ,r-rocr) - ("r-seqinr" ,r-seqinr))) - (home-page "https://cran.r-project.org/web/packages/gkmSVM") - (synopsis "Gapped-kmer support vector machine") - (description - "This R package provides tools for training gapped-kmer SVM classifiers -for DNA and protein sequences. This package supports several sequence -kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") - (license license:gpl2+))) - ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package @@ -6026,14 +6909,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) + "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -6525,14 +7408,14 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) + "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (arguments @@ -6547,7 +7430,8 @@ sequential way to mimic the manual gating strategy.") (string-append match "/libhdf5.a"))) #t))))) (inputs - `(("libxml2" ,libxml2))) + `(("libxml2" ,libxml2) + ("zlib" ,zlib))) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) @@ -6810,6 +7694,59 @@ accessibility data.") ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) +(define-public r-circrnaprofiler + (package + (name "r-circrnaprofiler") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "circRNAprofiler" version)) + (sha256 + (base32 + "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8")))) + (properties + `((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))) + (home-page + "https://github.com/Aufiero/circRNAprofiler") + (synopsis + "Computational framework for the downstream analysis of circular RNA's") + (description + "@code{r-circrnaprofiler} is a computational framework for a comprehensive +in silico analysis of @dfn{circular RNA} (circRNAs). This computational +framework allows to combine and analyze circRNAs previously detected by +multiple publicly available annotation-based circRNA detection tools. It +covers different aspects of circRNAs analysis from differential expression +analysis, evolutionary conservation, biogenesis to functional analysis.") + (license license:gpl3))) + (define-public r-cistopic (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") (revision "0")) @@ -7435,6 +8372,56 @@ data. This modified test allows for testing differential expression in qPCR data.") (license license:gpl2+))) +(define-public r-universalmotif + (package + (name "r-universalmotif") + (version "1.8.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "universalmotif" version)) + (sha256 + (base32 + "0pmi5mp5v0srr482vlkfmkp28bywq969fvv9g5kjl5rxki963zmr")))) + (properties + `((upstream-name . "universalmotif"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-reference-to-strip + (lambda _ + (substitute* "src/Makevars" + (("/usr/bin/strip") (which "strip")))))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-ggplot2" ,r-ggplot2) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) + ("r-rcpp" ,r-rcpp) + ("r-rcppthread" ,r-rcppthread) + ("r-rdpack" ,r-rdpack) + ("r-rlang" ,r-rlang) + ("r-s4vectors" ,r-s4vectors) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page + "https://bioconductor.org/packages/universalmotif/") + (synopsis + "Specific structures importer, modifier, and exporter for R") + (description + "This package allows importing most common @dfn{specific structure} +(motif) types into R for use by functions provided by other Bioconductor +motif-related packages. Motifs can be exported into most major motif formats +from various classes as defined by other Bioconductor packages. A suite of +motif and sequence manipulation and analysis functions are included, including +enrichment, comparison, P-value calculation, shuffling, trimming, higher-order +motifs, and others.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activedriverwgs @@ -7812,14 +8799,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.42.1") + (version "3.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "1853w19042c53whdnrfg1v8f07wpswf2si8q4613yrcamzg2zjkx")))) + "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -7853,14 +8840,14 @@ structures.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.28.0") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f")))) + "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -7873,7 +8860,7 @@ structures.") ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/TylerBackman/bioassayR") + (home-page "https://github.com/girke-lab/bioassayR") (synopsis "Cross-target analysis of small molecule bioactivity") (description "bioassayR is a computational tool that enables simultaneous analysis of @@ -8022,6 +9009,55 @@ microarray data.") monograph.") (license license:artistic2.0))) +(define-public r-bioccheck + (package + (name "r-bioccheck") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCheck" version)) + (sha256 + (base32 + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + (properties + `((upstream-name . "BiocCheck"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This package can be used by calling BiocCheck(<package>) from + ;; within R, or by running R CMD BiocCheck <package>. This phase + ;; makes sure the latter works. For this to work, the BiocCheck + ;; script must be somewhere on the PATH (not the R bin directory). + (add-after 'install 'install-bioccheck-subcommand + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest-dir (string-append out "/bin")) + (script-dir + (string-append out "/site-library/BiocCheck/script/"))) + (mkdir-p dest-dir) + (symlink (string-append script-dir "/checkBadDeps.R") + (string-append dest-dir "/checkBadDeps.R")) + (symlink (string-append script-dir "/BiocCheck") + (string-append dest-dir "/BiocCheck"))) + #t))))) + (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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocCheck") + (synopsis "Executes Bioconductor-specific package checks") + (description "This package contains tools to perform additional quality +checks on R packages that are to be submitted to the Bioconductor repository.") + (license license:artistic2.0))) + (define-public r-biocgraph (package (name "r-biocgraph") @@ -8047,6 +9083,62 @@ monograph.") different graph related packages produced by Bioconductor.") (license license:artistic2.0))) +(define-public r-biocstyle + (package + (name "r-biocstyle") + (version "2.18.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocStyle" version)) + (sha256 + (base32 + "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) + (properties + `((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))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocStyle") + (synopsis "Bioconductor formatting styles") + (description "This package provides standard formatting styles for +Bioconductor PDF and HTML documents. Package vignettes illustrate use and +functionality.") + (license license:artistic2.0))) + +(define-public r-biocviews + (package + (name "r-biocviews") + (version "1.58.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biocViews" version)) + (sha256 + (base32 + "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) + (properties + `((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))) + (home-page "https://bioconductor.org/packages/biocViews") + (synopsis "Bioconductor package categorization helper") + (description "The purpose of biocViews is to create HTML pages that +categorize packages in a Bioconductor package repository according to keywords, +also known as views, in a controlled vocabulary.") + (license license:artistic2.0))) + (define-public r-experimenthub (package (name "r-experimenthub") @@ -8081,6 +9173,33 @@ and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) +(define-public r-grohmm + (package + (name "r-grohmm") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "groHMM" version)) + (sha256 + (base32 + "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) + (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))) + (home-page "https://github.com/Kraus-Lab/groHMM") + (synopsis "GRO-seq analysis pipeline") + (description + "This package provides a pipeline for the analysis of GRO-seq data.") + (license license:gpl3+))) + (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") @@ -8592,19 +9711,46 @@ generated.") routines.") (license license:lgpl2.0+))) +(define-public r-s4vectors + (package + (name "r-s4vectors") + (version "0.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Vectors" version)) + (sha256 + (base32 + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + (properties + `((upstream-name . "S4Vectors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/S4Vectors") + (synopsis "S4 implementation of vectors and lists") + (description + "The S4Vectors package defines the @code{Vector} and @code{List} virtual +classes and a set of generic functions that extend the semantic of ordinary +vectors and lists in R. Package developers can easily implement vector-like +or list-like objects as concrete subclasses of @code{Vector} or @code{List}. +In addition, a few low-level concrete subclasses of general interest (e.g. +@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the +S4Vectors package itself.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on preprocessorcore, which is a ;; Bioconductor package. (define-public r-wgcna (package (name "r-wgcna") - (version "1.69") + (version "1.70-3") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f")))) + "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs @@ -8875,6 +10021,184 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +;; This package includes files that have been taken from kentutils. Some +;; parts of kentutils are not released under a free license, but this package +;; only uses files that are also found in the free parts of kentutils. +(define-public r-cner + (package + (name "r-cner") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "CNEr" version)) + (sha256 + (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c")))) + (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))) + (home-page "https://github.com/ge11232002/CNEr") + (synopsis "CNE Detection and Visualization") + (description + "This package provides tools for large-scale identification and +advanced visualization of sets of conserved noncoding elements.") + ;; For all files in src/ucsc "license is hereby granted for all use - + ;; public, private or commercial"; this includes those files that don't + ;; have a license header, because they are included in the free parts of + ;; the kentutils package. + (license (list license:gpl2 + (license:non-copyleft + "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE"))))) + +(define-public r-tfbstools + (package + (name "r-tfbstools") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TFBSTools" version)) + (sha256 + (base32 + "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha")))) + (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))) + (home-page "https://github.com/ge11232002/TFBSTools") + (synopsis "Transcription factor binding site (TFBS) analysis") + (description + "TFBSTools is a package for the analysis and manipulation of +transcription factor binding sites. It includes matrices conversion +between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight +Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also +scan putative TFBS from sequence/alignment, query JASPAR database and +provides a wrapper of de novo motif discovery software.") + (license license:gpl2))) + +(define-public r-motifmatchr + (package + (name "r-motifmatchr") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "motifmatchr" version)) + (sha256 + (base32 + "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z")))) + (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))) + (home-page "https://bioconductor.org/packages/motifmatchr") + (synopsis "Fast motif matching in R") + (description + "Quickly find motif matches for many motifs and many sequences. +This package wraps C++ code from the MOODS motif calling library.") + (license license:gpl3))) + +(define-public r-chromvar + (package + (name "r-chromvar") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chromVAR" version)) + (sha256 + (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819")))) + (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))) + (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html") + (synopsis "Determine chromatin variation across regions") + (description + "This package @code{r-chromvar} determines variation in chromatin +accessibility across sets of annotations or peaks. @code{r-chromvar} is +designed primarily for single-cell or sparse chromatin accessibility data like +single cell assay for transposase-accessible chromatin using +sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease +sequence (@code{DNAse-seq}) experiments.") + (license license:expat))) + (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") @@ -8942,13 +10266,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.18.3") + (version "1.18.6") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535")))) + "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9479,14 +10803,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) + "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -9707,6 +11031,44 @@ large-scale and fully automated analysis.") the earlier snpMatrix package, allowing for uncertainty in genotypes.") (license license:gpl3))) +(define-public r-chromstar + (package + (name "r-chromstar") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "chromstaR" version)) + (sha256 + (base32 + "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1")))) + (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))) + (home-page "https://github.com/ataudt/chromstaR") + (synopsis "Chromatin state analysis for ChIP-Seq data") + (description + "This package implements functions for combinatorial and differential +analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, +export to genome browser viewable files, and functi ons for enrichment +analyses.") + (license license:artistic2.0))) + (define-public r-sushi (package (name "r-sushi") |