;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) (properties `((upstream-name . 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Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) (define-public r-affycomp (package (name "r-affycomp") (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk")))) (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 "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyCompatible" version)) (sha256 (base32 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x")))) (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 "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b")))) (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 "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-affxparser (package (name "r-affxparser") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p")))) (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") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-httr" ,r-httr) ("r-xml" ,r-xml) ("r-xtable" ,r-xtable))) (home-page "https://bioconductor.org/packages/annotate") (synopsis "Annotation for microarrays") (description "This package provides R environments for the annotation of microarrays.") (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-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 . 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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 "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 "1sbhdpgabqbi749ixih8nlmq5id7sg8y6kkfj46r00642rc293ys")))) (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-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") (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr")))) (build-system r-build-system) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from the Human Protein Atlas project.") (license license:artistic2.0))) (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 . 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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-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 . 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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 . 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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 . 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(license license:lgpl2.0+))) (define-public r-qvalue (package (name "r-qvalue") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local @dfn{false discovery rate} (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) (define r-rcppnumerical (package (name "r-rcppnumerical") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (properties `((upstream-name . "RcppNumerical"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis "Rcpp integration for numerical computing libraries") (description "This package provides a collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-apeglm (package (name "r-apeglm") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs `(("r-emdbook" ,r-emdbook) ("r-genomicranges" ,r-genomicranges) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppnumerical" ,r-rcppnumerical) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.") (license license:gpl2))) (define-public r-greylistchip (package (name "r-greylistchip") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-mass" ,r-mass) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling.") (license license:artistic2.0))) (define-public r-diffbind (package (name "r-diffbind") (version "3.0.14") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 "1siabhjd0w7bb6v2gfhsm9j7c7c86z8m6lfsyl8p84h0zhjs2vrw")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap) ("r-apeglm" ,r-apeglm) ("r-ashr" ,r-ashr) ("r-biocparallel" ,r-biocparallel) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) ("r-greylistchip" ,r-greylistchip) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-rcolorbrewer" , r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper))) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description "This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.") (license license:artistic2.0))) (define-public r-ripseeker (package (name "r-ripseeker") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rsamtools" ,r-rsamtools) ("r-genomicalignments" ,r-genomicalignments) ("r-rtracklayer" ,r-rtracklayer))) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") (description "This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) (define-public r-multtest (package (name "r-multtest") (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) ("r-biocgenerics" ,r-biocgenerics) ("r-biobase" ,r-biobase) ("r-mass" ,r-mass))) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description "This package can do non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of T- and F-statistics (including T-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with T-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted P-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) (define-public r-graph (package (name "r-graph") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-ggm (package (name "r-ggm") (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "ggm" version)) (sha256 (base32 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-igraph" ,r-igraph))) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description "This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. (define-public r-perfmeas (package (name "r-perfmeas") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "PerfMeas" version)) (sha256 (base32 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-limma" ,r-limma) ("r-rbgl" ,r-rbgl))) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description "This package implements different performance measures for classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package (name "r-codedepends") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "CodeDepends" version)) (sha256 (base32 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) ("r-xml" ,r-xml))) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description "This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-chippeakanno (package (name "r-chippeakanno") (version "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) ("r-iranges" ,r-iranges) ("r-keggrest" ,r-keggrest) ("r-matrixstats" ,r-matrixstats) ("r-multtest" ,r-multtest) ("r-rbgl" ,r-rbgl) ("r-regioner" ,r-regioner) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-venndiagram" ,r-venndiagram))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ChIPpeakAnno") (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") (description "The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).") (license license:gpl2+))) (define-public r-matrixgenerics (package (name "r-matrixgenerics") (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) (propagated-inputs `(("r-matrixstats" ,r-matrixstats))) (home-page "https://bioconductor.org/packages/MatrixGenerics") (synopsis "S4 generic summary statistic functions for matrix-like objects") (description "This package provides S4 generic functions modeled after the @code{matrixStats} API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.") (license license:artistic2.0))) (define-public r-marray (package (name "r-marray") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray")))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma))) (home-page "https://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted microarray data. It also includes functions for data input, diagnostic plots, normalization and quality checking.") (license license:lgpl2.0+))) (define-public r-cghbase (package (name "r-cghbase") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-marray" ,r-marray))) (home-page "https://bioconductor.org/packages/CGHbase") (synopsis "Base functions and classes for arrayCGH data analysis") (description "This package contains functions and classes that are needed by the @code{arrayCGH} packages.") (license license:gpl2+))) (define-public r-cghcall (package (name "r-cghcall") (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-bayseq (package (name "r-bayseq") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "baySeq" version)) (sha256 (base32 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215")))) (properties `((upstream-name . "baySeq"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-edger" ,r-edger) ("r-genomicranges" ,r-genomicranges))) (home-page "https://bioconductor.org/packages/baySeq/") (synopsis "Bayesian analysis of differential expression patterns in count data") (description "This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.") (license license:gpl3))) (define-public r-chipcomp (package (name "r-chipcomp") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/ChIPComp") (synopsis "Quantitative comparison of multiple ChIP-seq datasets") (description "ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets.") ;; Any version of the GPL. (license license:gpl3+))) (define-public r-riboprofiling (package (name "r-riboprofiling") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-riboseqr (package (name "r-riboseqr") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "riboSeqR" version)) (sha256 (base32 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr")))) (properties `((upstream-name . "riboSeqR"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-bayseq" ,r-bayseq) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rsamtools" ,r-rsamtools) ("r-seqlogo" ,r-seqlogo))) (home-page "https://bioconductor.org/packages/riboSeqR/") (synopsis "Analysis of sequencing data from ribosome profiling experiments") (description "This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.") (license license:gpl3))) (define-public r-interactionset (package ;BROKEN (name "r-interactionset") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-genomicinteractions (package (name "r-genomicinteractions") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd")))) (properties `((upstream-name . 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(license license:lgpl2.0+))) (define-public r-glimma (package (name "r-glimma") (version "2.0.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv")))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) (propagated-inputs `(("r-deseq2" ,r-deseq2) ("r-edger" ,r-edger) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jsonlite" ,r-jsonlite) ("r-limma" ,r-limma) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description "This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.") (license license:lgpl3))) (define-public r-rots (package (name "r-rots") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-rcpp" ,r-rcpp))) (home-page "https://bioconductor.org/packages/ROTS/") (synopsis "Reproducibility-Optimized Test Statistic") (description "This package provides tools for calculating the @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing in omics data.") 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(license license:gpl2))) (define-public r-inspect (package (name "r-inspect") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-dnabarcodes (package (name "r-dnabarcodes") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DNABarcodes") (synopsis "Create and analyze DNA barcodes") (description "This package offers tools to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analyzed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e. assigned to their original reference barcode.") (license license:gpl2))) (define-public r-ruvseq (package (name "r-ruvseq") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-edaseq" ,r-edaseq) ("r-edger" ,r-edger) ("r-mass" ,r-mass))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/drisso/RUVSeq") (synopsis "Remove unwanted variation from RNA-Seq data") (description "This package implements methods to @dfn{remove unwanted variation} (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.") (license license:artistic2.0))) (define-public r-biocneighbors (package (name "r-biocneighbors") (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs `(("r-biocparallel" ,r-biocparallel) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp) ("r-rcpphnsw" ,r-rcpphnsw) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocNeighbors") (synopsis "Nearest Neighbor Detection for Bioconductor packages") (description "This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.") (license license:gpl3))) (define-public r-biocsingular (package (name "r-biocsingular") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-destiny (package (name "r-destiny") (version "3.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-ggplot-multistats" ,r-ggplot-multistats) ("r-ggplot2" ,r-ggplot2) ("r-ggthemes" ,r-ggthemes) ("r-irlba" ,r-irlba) ("r-knn-covertree" ,r-knn-covertree) ("r-matrix" ,r-matrix) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcpphnsw" ,r-rcpphnsw) ("r-rspectra" ,r-rspectra) ("r-scales" ,r-scales) ("r-scatterplot3d" ,r-scatterplot3d) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-smoother" ,r-smoother) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr) ("r-tidyselect" ,r-tidyselect) ("r-vim" ,r-vim))) (native-inputs `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion maps.") ;; Any version of the GPL (license license:gpl3+))) (define-public r-savr (package (name "r-savr") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-copynumber (package (name "r-copynumber") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/copynumber") (synopsis "Segmentation of single- and multi-track copy number data") (description "This package segments single- and multi-track copy number data by a penalized least squares regression method.") (license license:artistic2.0))) (define-public r-dnacopy (package (name "r-dnacopy") (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc")))) (properties `((upstream-name . 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(license license:expat))) ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package (name "r-mutoss") (version "0.1-12") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs `(("r-multcomp" ,r-multcomp) ("r-multtest" ,r-multtest) ("r-mvtnorm" ,r-mvtnorm) ("r-plotrix" ,r-plotrix))) (home-page "https://github.com/kornl/mutoss/") (synopsis "Unified multiple testing procedures") (description "This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.") ;; Any version of the GPL. (license (list license:gpl2+ license:gpl3+)))) ;; This is a CRAN package, but it depends on mutoss, which depends on multtest ;; from Bioconductor, so we put it here. (define-public r-metap (package (name "r-metap") (version "1.3") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) ("r-mutoss" ,r-mutoss) ("r-rdpack" ,r-rdpack) ("r-tfisher" ,r-tfisher))) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description "The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.") 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This package gives a choice of algorithms for interrogation of genomes with motifs from public sources: @enumerate @item a weighted-sum probability matrix; @item log-probabilities; @item weighted by relative entropy. @end enumerate This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.") (license license:gpl2+))) (define-public r-motifstack (package (name "r-motifstack") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-atacseqqc (package (name "r-atacseqqc") (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) (properties `((upstream-name . 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It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. The ATACseqQC package was developed to help users to quickly assess whether their ATAC-seq experiment is successful. It includes diagnostic plots of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.") (license license:gpl2+))) (define-public r-gofuncr (package (name "r-gofuncr") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq")))) (properties `((upstream-name . 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GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests: @enumerate @item the Wilcoxon rank-sum test that is used when genes are ranked, @item a binomial test that is used when genes are associated with two counts, and @item a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. @end enumerate To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.") (license license:gpl2+))) (define-public r-abaenrichment (package (name "r-abaenrichment") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs `(("r-abadata" ,r-abadata) ("r-data-table" ,r-data-table) ("r-gofuncr" ,r-gofuncr) ("r-gplots" ,r-gplots) ("r-gtools" ,r-gtools) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description "The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function @code{aba_enrich} integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.") (license license:gpl2+))) (define-public r-annotationfuncs (package (name "r-annotationfuncs") (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-dbi" ,r-dbi))) (home-page "https://www.iysik.com/r/annotationfuncs") (synopsis "Annotation translation functions") (description "This package provides functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. @code{org.Bt.eg.db}).") (license license:gpl2))) (define-public r-annotationtools (package (name "r-annotationtools") (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase))) (home-page "https://bioconductor.org/packages/annotationTools/") (synopsis "Annotate microarrays and perform gene expression analyses") (description "This package provides functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).") ;; Any version of the GPL. (license (list license:gpl2+)))) (define-public r-allelicimbalance (package (name "r-allelicimbalance") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-aucell (package (name "r-aucell") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-gseabase" ,r-gseabase) ("r-mixtools" ,r-mixtools) ("r-r-utils" ,r-r-utils) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AUCell/") (synopsis "Analysis of gene set activity in single-cell RNA-seq data") (description "AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area Under the Curve} (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.") (license license:gpl3))) (define-public r-ebimage (package (name "r-ebimage") (version "4.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww")))) (properties `((upstream-name . 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(license license:lgpl2.1+))) (define-public r-yamss (package (name "r-yamss") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-ebimage" ,r-ebimage) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) ("r-mzr" ,r-mzr) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/yamss") (synopsis "Tools for high-throughput metabolomics") (description "This package provides tools to analyze and visualize high-throughput metabolomics data acquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.") (license license:artistic2.0))) (define-public r-gtrellis (package (name "r-gtrellis") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw")))) (build-system r-build-system) (propagated-inputs `(("r-circlize" ,r-circlize) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-iranges" ,r-iranges))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/jokergoo/gtrellis") (synopsis "Genome level Trellis layout") (description "Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.") (license license:expat))) (define-public r-somaticsignatures (package (name "r-somaticsignatures") (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggbio" ,r-ggbio) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-nmf" ,r-nmf) ("r-pcamethods" ,r-pcamethods) ("r-proxy" ,r-proxy) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/juliangehring/SomaticSignatures") (synopsis "Somatic signatures") (description "This package identifies mutational signatures of @dfn{single nucleotide variants} (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.") (license license:expat))) (define-public r-yapsa (package (name "r-yapsa") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-circlize" ,r-circlize) ("r-complexheatmap" ,r-complexheatmap) ("r-corrplot" ,r-corrplot) ("r-dendextend" ,r-dendextend) ("r-doparallel" ,r-doparallel) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-getoptlong" ,r-getoptlong) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-gtrellis" ,r-gtrellis) ("r-keggrest" ,r-keggrest) ("r-limsolve" ,r-limsolve) ("r-magrittr" ,r-magrittr) ("r-pmcmr" ,r-pmcmr) ("r-pracma" ,r-pracma) ("r-reshape2" ,r-reshape2) ("r-somaticsignatures" ,r-somaticsignatures) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/YAPSA/") (synopsis "Yet another package for signature analysis") (description "This package provides functions and routines useful in the analysis of somatic signatures (cf. 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The main function @code{gcrma} converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. 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Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.") (license license:gpl3+))) (define-public r-yarn (package (name "r-yarn") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biomart" ,r-biomart) ("r-downloader" ,r-downloader) ("r-edger" ,r-edger) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-matrixstats" ,r-matrixstats) ("r-preprocesscore" ,r-preprocesscore) ("r-quantro" ,r-quantro) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-readr" ,r-readr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/yarn/") (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") (description "Expedite large RNA-Seq analyses using a combination of previously developed tools. 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(license license:artistic2.0))) (define-public r-roar (package (name "r-roar") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description "This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.") 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It 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-wrench (package (name "r-wrench") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs `(("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/HCBravoLab/Wrench") (synopsis "Wrench normalization for sparse count data") (description "Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.") 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(license license:lgpl3+))) (define-public r-webbioc (package (name "r-webbioc") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) ("perl" ,perl))) (propagated-inputs `(("r-affy" ,r-affy) ("r-annaffy" ,r-annaffy) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-gcrma" ,r-gcrma) ("r-multtest" ,r-multtest) ("r-qvalue" ,r-qvalue) ("r-vsn" ,r-vsn))) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description "This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) (define-public r-zfpkm (package (name "r-zfpkm") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description "This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).") (license license:gpl3))) (define-public r-rbowtie2 (package (name "r-rbowtie2") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description "This package provides an R wrapper of the popular @code{bowtie2} sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for rapid adapter trimming, identification, and read merging.") 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(license license:asl2.0))) (define-public r-arrmnormalization (package (name "r-arrmnormalization") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description "This is a package to perform the @dfn{Adaptive Robust Regression method} (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.") 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Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.") (license license:artistic2.0))) (define-public r-rhisat2 (package (name "r-rhisat2") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ (substitute* "src/Makefile" (("`hostname`") "guix") (("`date`") "0") ;; Avoid shelling out to "which". (("^CC =.*") (which "gcc")) (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-sgseq" ,r-sgseq))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description "This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.") (license license:gpl3))) (define-public r-quasr (package (name "r-quasr") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-rbowtie" ,r-rbowtie) ("r-rhisat2" ,r-rhisat2) ("r-rhtslib" ,r-rhtslib) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shortread" ,r-shortread))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description "This package provides a framework for the quantification and analysis of short genomic reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.") (license license:gpl2))) (define-public r-rqc (package (name "r-rqc") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biocstyle" ,r-biocstyle) ("r-biostrings" ,r-biostrings) ("r-biovizbase" ,r-biovizbase) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfiles" ,r-genomicfiles) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-knitr" ,r-knitr) ("r-markdown" ,r-markdown) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) ("r-shortread" ,r-shortread))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description "Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) (define-public r-birewire (package (name "r-birewire") (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-slam" ,r-slam) ("r-tsne" ,r-tsne))) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.") (license license:gpl3))) (define-public r-birta (package (name "r-birta") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limma" ,r-limma) ("r-mass" ,r-mass))) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description "Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-qqman" ,r-qqman) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description "This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.") (license license:expat))) (define-public r-ropls (package (name "r-ropls") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. This package provides imlementations of PCA, PLS, and OPLS for multivariate analysis and feature selection of omics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients).") (license license:cecill))) (define-public r-biosigner (package (name "r-biosigner") (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description "Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationhub" ,r-annotationhub) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-readr" ,r-readr) ("r-regioner" ,r-regioner) ("r-reshape2" ,r-reshape2) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.") (license license:gpl3))) (define-public r-rsubread (package (name "r-rsubread") (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description "This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) (define-public r-flowutils (package (name "r-flowutils") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-flowcore" ,r-flowcore) ("r-graph" ,r-graph) ("r-runit" ,r-runit) ("r-xml" ,r-xml))) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description "This package provides utilities for flow cytometry data.") (license license:artistic2.0))) (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs `(("r-all" ,r-all) ("r-biobase" ,r-biobase) ("r-cluster" ,r-cluster))) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description "This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) (define-public r-cytolib (package (name "r-cytolib") (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars.in" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (native-inputs `(("r-knitr" ,r-knitr) ("pkg-config" ,pkg-config))) (propagated-inputs `(("r-bh" ,r-bh) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib))) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description "This package provides the core data structure and API to represent and interact with gated cytometry data.") (license license:artistic2.0))) (define-public r-flowcore (package (name "r-flowcore") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rprotobuflib" ,r-rprotobuflib) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description "This package provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) (define-public r-flowmeans (package (name "r-flowmeans") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-feature" ,r-feature) ("r-flowcore" ,r-flowcore) ("r-rrcov" ,r-rrcov))) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description "This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) (define-public r-ncdfflow (package (name "r-ncdfflow") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-flowcore" ,r-flowcore) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) (define-public r-ggcyto (package (name "r-ggcyto") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-hexbin" ,r-hexbin) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description "With the dedicated fortify method implemented for @code{flowSet}, @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper and some custom layers also make it easy to add gates and population statistics to the plot.") (license license:artistic2.0))) (define-public r-flowviz (package (name "r-flowviz") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-flowcore" ,r-flowcore) ("r-hexbin" ,r-hexbin) ("r-idpmisc" ,r-idpmisc) ("r-kernsmooth" ,r-kernsmooth) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) (define-public r-flowclust (package (name "r-flowclust") (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-corpcor" ,r-corpcor) ("r-ellipse" ,r-ellipse) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) (inputs `(("gsl" ,gsl))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description "This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.") (license license:artistic2.0))) ;; TODO: this package bundles an old version of protobuf. It's not easy to ;; make it use our protobuf package instead. (define-public r-rprotobuflib (package (name "r-rprotobuflib") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) #t))))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description "This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.") (license license:bsd-3))) (define-public r-flowworkspace (package (name "r-flowworkspace") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-matrixstats" ,r-matrixstats) ("r-ncdfflow" ,r-ncdfflow) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description "This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.") (license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cluster" ,r-cluster) ("r-fda" ,r-fda) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-kernsmooth" ,r-kernsmooth) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rrcov" ,r-rrcov))) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description "This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the @code{flowCore} package.") (license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-data-table" ,r-data-table) ("r-flowclust" ,r-flowclust) ("r-flowcore" ,r-flowcore) ("r-flowstats" ,r-flowstats) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-graph" ,r-graph) ("r-gtools" ,r-gtools) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-r-utils" ,r-r-utils) ("r-rbgl" ,r-rbgl) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rrcov" ,r-rrcov))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars.in" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (inputs `(("libxml2" ,libxml2))) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggcyto" ,r-ggcyto) ("r-graph" ,r-graph) ("r-jsonlite" ,r-jsonlite) ("r-lattice" ,r-lattice) ("r-opencyto" ,r-opencyto) ("r-plyr" ,r-plyr) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-runit" ,r-runit) ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) ("r-xml2" ,r-xml2) ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description "This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.") (license license:artistic2.0))) (define-public r-flowsom (package (name "r-flowsom") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description "FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.") (license license:gpl2+))) (define-public r-mixomics (package (name "r-mixomics") (version "6.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) ("r-ggrepel" ,r-ggrepel) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description "mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gmodels" ,r-gmodels) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-mixomics" ,r-mixomics) ("r-moments" ,r-moments) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description "The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined 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 "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) (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))) (native-inputs `(("r-knitr" ,r-knitr))) (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") (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-glasso" ,r-glasso) ("r-gviz" ,r-gviz) ("r-igraph" ,r-igraph) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-monocle" ,r-monocle) ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vgam" ,r-vgam))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description "Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs `(("r-monocle3" ,r-monocle3) ,@(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")) (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") (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs `(("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (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 "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs `(("r-knitr" ,r-knitr))) (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 "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-illuminahumanmethylation450kanno-ilmn12-hg19" ,r-illuminahumanmethylation450kanno-ilmn12-hg19) ("r-illuminaio" ,r-illuminaio) ("r-limma" ,r-limma) ("r-lumi" ,r-lumi) ("r-matrixstats" ,r-matrixstats) ("r-methylumi" ,r-methylumi) ("r-roc" ,r-roc))) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description "The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. 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 "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) (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 . "gdsfmt"))) (build-system r-build-system) (inputs `(("lz4" ,lz4) ("xz" ,xz) ("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") (description "This package provides a high-level R interface to CoreArray @dfn{Genomic Data Structure} (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The @code{gdsfmt} package offers efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. 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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-gdsfmt" ,r-gdsfmt) ("r-geoquery" ,r-geoquery) ("r-methylumi" ,r-methylumi) ("r-minfi" ,r-minfi) ("r-watermelon" ,r-watermelon))) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) (define-public r-seqbias (package (name "r-seqbias") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-rhtslib" ,r-rhtslib))) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure 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 `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-bsgenome" ,r-bsgenome) ("r-biostrings" ,r-biostrings))) (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") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs `(("r-rjava" ,r-rjava) ("r-rsamtools" ,r-rsamtools) ("r-seqbias" ,r-seqbias))) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description "This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.") (license license:gpl2))) (define-public r-wavcluster (package (name "r-wavcluster") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) (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 integrates 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 "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-wavetiling (package (name "r-wavetiling") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-genomegraphs" ,r-genomegraphs) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-oligo" ,r-oligo) ("r-oligoclasses" ,r-oligoclasses) ("r-preprocesscore" ,r-preprocesscore) ("r-waveslim" ,r-waveslim))) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description "This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.") (license license:gpl2+))) (define-public r-variancepartition (package (name "r-variancepartition") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) (properties `((upstream-name . 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The package includes dream differential expression analysis for repeated measures.") (license license:gpl2+))) (define-public r-htqpcr (package (name "r-htqpcr") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).") (license license:artistic2.0))) (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) (properties `((upstream-name . 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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 (package (name "r-activedriverwgs") (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "ActiveDriverWGS" version)) (sha256 (base32 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say")))) (properties `((upstream-name . "ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description "This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.") (license license:gpl3))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-activepathways (package (name "r-activepathways") (version "1.0.2") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-ggplot2" ,r-ggplot2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActivePathways/") (synopsis "Multivariate pathway enrichment analysis") (description "This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.") (license license:gpl3))) (define-public r-bgmix (package (name "r-bgmix") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) (propagated-inputs `(("r-kernsmooth" ,r-kernsmooth))) (home-page "https://bioconductor.org/packages/BGmix/") (synopsis "Bayesian models for differential gene expression") (description "This package provides fully Bayesian mixture models for differential gene expression.") (license license:gpl2))) (define-public r-bgx (package (name "r-bgx") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im")))) (properties `((upstream-name . 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This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.") (license license:gpl3))) (define-public r-bicare (package (name "r-bicare") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-gseabase" ,r-gseabase) ("r-multtest" ,r-multtest))) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description "This is a package for biclustering analysis and exploration of results.") (license license:gpl2))) (define-public r-bifet (package (name "r-bifet") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs `(("r-genomicranges" ,r-genomicranges) ("r-poibin" ,r-poibin))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiFET") (synopsis "Bias-free footprint enrichment test") (description "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. 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These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.") (license license:artistic2.0))) (define-public r-biocio (package (name "r-biocio") (version "1.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18")))) (properties `((upstream-name . 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Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin. This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.") (license license:artistic2.0))) (define-public r-ggbio (package (name "r-ggbio") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; See https://github.com/tengfei/ggbio/issues/117 ;; This fix will be included in the next release. 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The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.") (license license:artistic2.0))) (define-public r-gqtlbase (package (name "r-gqtlbase") (version "1.21.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases ;; This is an upstream bug. (add-after 'unpack 'fix-imports (lambda _ (substitute* "NAMESPACE" ((".*maxffmode.*") "") (("importFrom\\(ff,.*") "import(ff)\n")) #t))))) (propagated-inputs `(("r-batchjobs" ,r-batchjobs) ("r-bbmisc" ,r-bbmisc) ("r-biocgenerics" ,r-biocgenerics) ("r-bit" ,r-bit) ("r-doparallel" ,r-doparallel) ("r-ff" ,r-ff) ("r-ffbase" ,r-ffbase) ("r-foreach" ,r-foreach) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gQTLBase") (synopsis "Infrastructure for eQTL, mQTL and similar studies") (description "The purpose of this package is to simplify the storage and interrogation of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL, and more.") (license license:artistic2.0))) (define-public r-gqtlstats (package (name "r-gqtlstats") (version "1.21.3") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-gviz (package (name "r-gviz") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-biovizbase" ,r-biovizbase) ("r-bsgenome" ,r-bsgenome) ("r-digest" ,r-digest) ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-matrixstats" ,r-matrixstats) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Gviz") (synopsis "Plotting data and annotation information along genomic coordinates") (description "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.") (license license:artistic2.0))) (define-public r-gwascat (package (name "r-gwascat") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocfilecache" ,r-biocfilecache) ("r-biostrings" ,r-biostrings) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-readr" ,r-readr) ("r-s4vectors" ,r-s4vectors) ("r-snpstats" ,r-snpstats) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/gwascat") (synopsis "Tools for data in the EMBL-EBI GWAS catalog") (description "This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog.") (license license:artistic2.0))) (define-public r-kegggraph (package (name "r-kegggraph") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-rcurl" ,r-rcurl) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/KEGGgraph") (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor") (description "@code{r-kegggraph} is an interface between Kegg Pathway database and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated kgml (Kegg XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.") (license license:gpl2+))) (define-public r-ldblock (package (name "r-ldblock") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75) ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-httr" ,r-httr) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) ("r-snpstats" ,r-snpstats) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ldblock") (synopsis "Data structures for linkage disequilibrium measures in populations") (description "This package defines data structures for @dfn{linkage disequilibrium} (LD) measures in populations. Its purpose is to simplify handling of existing population-level data for the purpose of flexibly defining LD blocks.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on r-snpstats, which is a ;; Bioconductor package. (define-public r-ldheatmap (package (name "r-ldheatmap") (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "LDheatmap" version)) (sha256 (base32 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7")))) (properties `((upstream-name . "LDheatmap"))) (build-system r-build-system) (propagated-inputs `(("r-genetics" ,r-genetics) ("r-rcpp" ,r-rcpp) ("r-snpstats" ,r-snpstats))) (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html") (synopsis "Graphical display of pairwise linkage disequilibria between SNPs") (description "This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.") (license license:gpl3))) (define-public r-pathview (package (name "r-pathview") (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-graph" ,r-graph) ("r-kegggraph" ,r-kegggraph) ("r-keggrest" ,r-keggrest) ("r-org-hs-eg-db" ,r-org-hs-eg-db) ("r-png" ,r-png) ("r-rgraphviz" ,r-rgraphviz) ("r-xml" ,r-xml))) (home-page "https://pathview.uncc.edu/") (synopsis "Tool set for pathway based data integration and visualization") (description "@code{r-pathview} is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. This package automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, @code{r-pathview} also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) (define-public r-snpstats (package (name "r-snpstats") (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-matrix" ,r-matrix) ("r-survival" ,r-survival) ("r-zlibbioc" ,r-zlibbioc))) (home-page "https://bioconductor.org/packages/snpStats") (synopsis "Methods for SNP association studies") (description "This package provides classes and statistical methods for large @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.") (license license:gpl3))) (define-public r-sushi (package (name "r-sushi") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p")))) (properties `((upstream-name . 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