diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 937 |
1 files changed, 917 insertions, 20 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 74620a2cbe..7b0405427c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -31,7 +31,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) - #:use-module (gnu packages haskell) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) @@ -50,21 +50,14 @@ (version "1.4.0") (source (origin (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Celegans.UCSC.ce6_" - version ".tar.gz")) + (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" + version 'annotation)) (sha256 (base32 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) (properties `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) (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 `(("r-bsgenome" ,r-bsgenome))) (home-page @@ -532,6 +525,28 @@ annotations for the genome of the model mouse Mus musculus.") by UCSC (hg19, February 2009) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-ensdb-hsapiens-v75 + (package + (name "r-ensdb-hsapiens-v75") + (version "2.99.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) + (sha256 + (base32 + "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) + (properties + `((upstream-name . "EnsDb.Hsapiens.v75"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ensembldb" ,r-ensembldb))) + (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") + (synopsis "Ensembl based annotation package") + (description + "This package exposes an annotation database generated from Ensembl.") + (license license:artistic2.0))) + (define-public r-genelendatabase (package (name "r-genelendatabase") @@ -686,6 +701,31 @@ the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.") (license license:artistic2.0))) +(define-public r-txdb-celegans-ucsc-ce6-ensgene + (package + (name "r-txdb-celegans-ucsc-ce6-ensgene") + (version "3.2.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" + version 'annotation)) + (sha256 + (base32 + "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) + (properties + `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicfeatures" ,r-genomicfeatures))) + (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") + (synopsis "Annotation package for C elegans TxDb objects") + (description + "This package exposes a C elegans annotation database generated from UCSC +by exposing these as TxDb objects.") + (license license:artistic2.0))) + (define-public r-fdb-infiniummethylation-hg19 (package (name "r-fdb-infiniummethylation-hg19") @@ -770,6 +810,28 @@ annotations.") Disease Ontology.") (license license:artistic2.0))) +(define-public r-pfam-db + (package + (name "r-pfam-db") + (version "3.8.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "PFAM.db" version 'annotation)) + (sha256 + (base32 + "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) + (properties `((upstream-name . "PFAM.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/PFAM.db") + (synopsis "Set of protein ID mappings for PFAM") + (description + "This package provides a set of protein ID mappings for PFAM, assembled +using data from public repositories.") + (license license:artistic2.0))) + ;;; Experiment data @@ -895,6 +957,29 @@ jointly normalized data that are available here. The data are presented in the form of an @code{exprSet} object.") (license license:artistic2.0))) +(define-public r-affydata + (package + (name "r-affydata") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affydata" version 'experiment)) + (sha256 + (base32 + "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) + (properties `((upstream-name . "affydata"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy))) + (home-page "https://bioconductor.org/packages/affydata/") + (synopsis "Affymetrix data for demonstration purposes") + (description + "This package provides example datasets that represent 'real world +examples' of Affymetrix data, unlike the artificial examples included in the +package @code{affy}.") + (license license:gpl2+))) + ;;; Packages @@ -918,6 +1003,147 @@ the form of an @code{exprSet} object.") packages.") (license license:artistic2.0))) +(define-public r-affycomp + (package + (name "r-affycomp") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affycomp" version)) + (sha256 + (base32 + "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n")))) + (properties `((upstream-name . "affycomp"))) + (build-system r-build-system) + (propagated-inputs `(("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/affycomp/") + (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") + (description + "The package contains functions that can be used to compare expression +measures for Affymetrix Oligonucleotide Arrays.") + (license license:gpl2+))) + +(define-public r-affycompatible + (package + (name "r-affycompatible") + (version "1.44.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AffyCompatible" version)) + (sha256 + (base32 + "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs")))) + (properties + `((upstream-name . "AffyCompatible"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biostrings" ,r-biostrings) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/AffyCompatible/") + (synopsis "Work with Affymetrix GeneChip files") + (description + "This package provides an interface to Affymetrix chip annotation and +sample attribute files. The package allows an easy way for users to download +and manage local data bases of Affynmetrix NetAffx annotation files. It also +provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip +Command Console} (AGCC)-compatible sample annotation files.") + (license license:artistic2.0))) + +(define-public r-affycontam + (package + (name "r-affycontam") + (version "1.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affyContam" version)) + (sha256 + (base32 + "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp")))) + (properties `((upstream-name . "affyContam"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-affydata" ,r-affydata) + ("r-biobase" ,r-biobase))) + (home-page "https://bioconductor.org/packages/affyContam/") + (synopsis "Structured corruption of Affymetrix CEL file data") + (description + "Microarray quality assessment is a major concern of microarray analysts. +This package provides some simple approaches to in silico creation of quality +problems in CEL-level data to help evaluate performance of quality metrics.") + (license license:artistic2.0))) + +(define-public r-affycoretools + (package + (name "r-affycoretools") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affycoretools" version)) + (sha256 + (base32 + "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s")))) + (properties `((upstream-name . "affycoretools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affy" ,r-affy) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-edger" ,r-edger) + ("r-gcrma" ,r-gcrma) + ("r-ggplot2" ,r-ggplot2) + ("r-gostats" ,r-gostats) + ("r-gplots" ,r-gplots) + ("r-hwriter" ,r-hwriter) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-oligoclasses" ,r-oligoclasses) + ("r-reportingtools" ,r-reportingtools) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-xtable" ,r-xtable))) + (home-page "https://bioconductor.org/packages/affycoretools/") + (synopsis "Functions for analyses with Affymetrix GeneChips") + (description + "This package provides various wrapper functions that have been written +to streamline the more common analyses that a Biostatistician might see.") + (license license:artistic2.0))) + +(define-public r-affxparser + (package + (name "r-affxparser") + (version "1.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "affxparser" version)) + (sha256 + (base32 + "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33")))) + (properties `((upstream-name . "affxparser"))) + (build-system r-build-system) + (home-page "https://github.com/HenrikBengtsson/affxparser") + (synopsis "Affymetrix File Parsing SDK") + (description + "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, +BAR). It provides methods for fast and memory efficient parsing of Affymetrix +files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files +are supported. Currently, there are methods for reading @dfn{chip definition +file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read +either in full or in part. For example, probe signals from a few probesets +can be extracted very quickly from a set of CEL files into a convenient list +structure.") + ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is + ;; under LGPLv2+. + (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) + (define-public r-annotate (package (name "r-annotate") @@ -966,14 +1192,14 @@ the Human Protein Atlas project.") (define-public r-regioner (package (name "r-regioner") - (version "1.16.2") + (version "1.16.5") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q")))) + "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -992,6 +1218,54 @@ customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) +(define-public r-reportingtools + (package + (name "r-reportingtools") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ReportingTools" version)) + (sha256 + (base32 + "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc")))) + (properties + `((upstream-name . "ReportingTools"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-category" ,r-category) + ("r-deseq2" ,r-deseq2) + ("r-edger" ,r-edger) + ("r-ggbio" ,r-ggbio) + ("r-ggplot2" ,r-ggplot2) + ("r-gostats" ,r-gostats) + ("r-gseabase" ,r-gseabase) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-knitr" ,r-knitr) + ("r-lattice" ,r-lattice) + ("r-limma" ,r-limma) + ("r-pfam-db" ,r-pfam-db) + ("r-r-utils" ,r-r-utils) + ("r-xml" ,r-xml))) + (home-page "https://bioconductor.org/packages/ReportingTools/") + (synopsis "Tools for making reports in various formats") + (description + "The ReportingTools package enables users to easily display reports of +analysis results generated from sources such as microarray and sequencing +data. The package allows users to create HTML pages that may be viewed on a +web browser, or in other formats. Users can generate tables with sortable and +filterable columns, make and display plots, and link table entries to other +data sources such as NCBI or larger plots within the HTML page. Using the +package, users can also produce a table of contents page to link various +reports together for a particular project that can be viewed in a web +browser.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") @@ -1017,6 +1291,75 @@ region sets and other genomic features.") "This package provides functions for plotting genomic data.") (license license:artistic2.0))) +(define-public r-oligoclasses + (package + (name "r-oligoclasses") + (version "1.46.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "oligoClasses" version)) + (sha256 + (base32 + "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72")))) + (properties `((upstream-name . "oligoClasses"))) + (build-system r-build-system) + (propagated-inputs + `(("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-ff" ,r-ff) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/oligoClasses/") + (synopsis "Classes for high-throughput arrays") + (description + "This package contains class definitions, validity checks, and +initialization methods for classes used by the @code{oligo} and @code{crlmm} +packages.") + (license license:gpl2+))) + +(define-public r-oligo + (package + (name "r-oligo") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "oligo" version)) + (sha256 + (base32 + "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df")))) + (properties `((upstream-name . "oligo"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-affxparser" ,r-affxparser) + ("r-affyio" ,r-affyio) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-dbi" ,r-dbi) + ("r-ff" ,r-ff) + ("r-oligoclasses" ,r-oligoclasses) + ("r-preprocesscore" ,r-preprocesscore) + ("r-rsqlite" ,r-rsqlite) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/oligo/") + (synopsis "Preprocessing tools for oligonucleotide arrays") + (description + "This package provides a package to analyze oligonucleotide +arrays (expression/SNP/tiling/exon) at probe-level. It currently supports +Affymetrix (CEL files) and NimbleGen arrays (XYS files).") + (license license:lgpl2.0+))) + (define-public r-qvalue (package (name "r-qvalue") @@ -2977,14 +3320,14 @@ phenotype of interest.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c")))) + "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) @@ -3848,14 +4191,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y")))) + "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) @@ -4841,14 +5184,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "1.34.6") + (version "1.34.7") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0nnfh4hnrs5kd72m8c50cidbsxjz12szw2vynpmg8q0wpd99q550")))) + "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -5000,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.8.0") + (version "6.8.5") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "1f08jx35amn3sfcmqb96mjxxsm6dnpzhff625z758x1992wj4zsk")))) + "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -5089,6 +5432,41 @@ by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) +(define-public r-rcistarget + (package + (name "r-rcistarget") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RcisTarget" version)) + (sha256 + (base32 + "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd")))) + (properties `((upstream-name . "RcisTarget"))) + (build-system r-build-system) + (propagated-inputs + `(("r-aucell" ,r-aucell) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-feather" ,r-feather) + ("r-gseabase" ,r-gseabase) + ("r-r-utils" ,r-r-utils) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://aertslab.org/#scenic") + (synopsis "Identify transcription factor binding motifs enriched on a gene list") + (description + "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) +over-represented on a gene list. In a first step, RcisTarget selects DNA +motifs that are significantly over-represented in the surroundings of the +@dfn{transcription start site} (TSS) of the genes in the gene-set. This is +achieved by using a database that contains genome-wide cross-species rankings +for each motif. The motifs that are then annotated to TFs and those that have +a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for +each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. +genes in the gene-set that are ranked above the leading edge).") + (license license:gpl3))) + (define-public r-cicero (package (name "r-cicero") @@ -5151,3 +5529,522 @@ accessibility data.") `(("r-monocle3" ,r-monocle3) ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) + +(define-public r-cistopic + (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") + (revision "0")) + (package + (name "r-cistopic") + (version (git-version "0.2.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/aertslab/cisTopic.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) + (build-system r-build-system) + (propagated-inputs + `(("r-aucell" ,r-aucell) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-dosnow" ,r-dosnow) + ("r-dt" ,r-dt) + ("r-feather" ,r-feather) + ("r-fitdistrplus" ,r-fitdistrplus) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-lda" ,r-lda) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-rcistarget" ,r-rcistarget) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/aertslab/cisTopic") + (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") + (description + "The sparse nature of single cell epigenomics data can be overruled using +probabilistic modelling methods such as @dfn{Latent Dirichlet +Allocation} (LDA). This package allows the probabilistic modelling of +cis-regulatory topics (cisTopics) from single cell epigenomics data, and +includes functionalities to identify cell states based on the contribution of +cisTopics and explore the nature and regulatory proteins driving them.") + (license license:gpl3)))) + +(define-public r-genie3 + (package + (name "r-genie3") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GENIE3" version)) + (sha256 + (base32 + "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx")))) + (properties `((upstream-name . "GENIE3"))) + (build-system r-build-system) + (propagated-inputs `(("r-reshape2" ,r-reshape2))) + (home-page "https://bioconductor.org/packages/GENIE3") + (synopsis "Gene network inference with ensemble of trees") + (description + "This package implements the GENIE3 algorithm for inferring gene +regulatory networks from expression data.") + (license license:gpl2+))) + +(define-public r-roc + (package + (name "r-roc") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ROC" version)) + (sha256 + (base32 + "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c")))) + (properties `((upstream-name . "ROC"))) + (build-system r-build-system) + (home-page "https://www.bioconductor.org/packages/ROC/") + (synopsis "Utilities for ROC curves") + (description + "This package provides utilities for @dfn{Receiver Operating +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 `(("r-minfi" ,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") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "wateRmelon" version)) + (sha256 + (base32 + "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z")))) + (properties `((upstream-name . 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This package provides 15 flavours of betas and three performance +metrics, with methods for objects produced by the @code{methylumi} and +@code{minfi} packages.") + (license license:gpl3))) + +(define-public r-gdsfmt + (package + (name "r-gdsfmt") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "gdsfmt" version)) + (sha256 + (base32 + "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy")) + (modules '((guix build utils))) + ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build + ;; them and link with system libraries instead. + (snippet + '(begin + (for-each delete-file-recursively + '("src/LZ4" + "src/XZ" + "src/ZLIB")) + (substitute* "src/Makevars" + (("all: \\$\\(SHLIB\\)") "all:") + (("\\$\\(SHLIB\\): liblzma.a") "") + (("(ZLIB|LZ4)/.*") "") + (("CoreArray/dVLIntGDS.cpp.*") + "CoreArray/dVLIntGDS.cpp") + (("CoreArray/dVLIntGDS.o.*") + "CoreArray/dVLIntGDS.o") + (("PKG_LIBS = ./liblzma.a") + "PKG_LIBS = -llz4")) + (substitute* "src/CoreArray/dStream.h" + (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) + (string-append "include <" header ">"))) + #t)))) + (properties `((upstream-name . 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It is also allowed to read a GDS file in parallel +with multiple R processes supported by the package @code{parallel}.") + (license license:lgpl3))) + +(define-public r-bigmelon + (package + (name "r-bigmelon") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bigmelon" version)) + (sha256 + (base32 + "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9")))) + (properties `((upstream-name . 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The protein binding sites (clusters) are then +resolved at high resolution and cluster statistics are estimated using a +rigorous Bayesian framework. Post-processing of the results, data export for +UCSC genome browser visualization and motif search analysis are provided. In +addition, the package allows to integrate RNA-Seq data to estimate the False +Discovery Rate of cluster detection. Key functions support parallel multicore +computing. While wavClusteR was designed for PAR-CLIP data analysis, it can +be applied to the analysis of other NGS data obtained from experimental +procedures that induce nucleotide substitutions (e.g. BisSeq).") + (license license:gpl2))) + +(define-public r-timeseriesexperiment + (package + (name "r-timeseriesexperiment") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TimeSeriesExperiment" version)) + (sha256 + (base32 + "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y")))) + (properties + `((upstream-name . 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The package also +provides methods for retrieving enriched pathways.") + (license license:lgpl3+))) + +(define-public r-variantfiltering + (package + (name "r-variantfiltering") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "VariantFiltering" version)) + (sha256 + (base32 + "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17")))) + (properties + `((upstream-name . 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Another +strength of GenomeGraphs is to plot different data types such as array CGH, +gene expression, sequencing and other data, together in one plot using the +same genome coordinate system.") + (license license:artistic2.0))) + +(define-public r-wavetiling + (package + (name "r-wavetiling") + (version "1.26.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "waveTiling" version)) + (sha256 + (base32 + "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir")))) + (properties `((upstream-name . 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The +package includes dream differential expression analysis for repeated +measures.") + (license license:gpl2+))) |