;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2023 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2022 Efraim Flashner ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet ;;; Copyright © 2023 Navid Afkhami ;;; ;;; 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 gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages docker) #: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 java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #: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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(license license:gpl3+))) (define-public r-adam (package (name "r-adam") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dt r-go-db r-keggrest r-knitr r-pbapply r-rcpp r-stringr r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ADAM") (synopsis "Gene activity and diversity analysis module") (description "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions. 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It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.") (license license:gpl2))) (define-public r-deseq (package (name "r-deseq") (version "1.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1")))) (properties `((upstream-name . 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The package is designed to deal with sequencing data from @dfn{Reduced representation bisulfite sequencing} (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) (define-public r-mmuphin (package (name "r-mmuphin") (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")) ;; Delete generated files. (snippet '(for-each delete-file '("inst/doc/MMUPHin.R" "inst/doc/MMUPHin.html"))))) (properties `((upstream-name . 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(propagated-inputs (list r-cowplot r-biocstyle r-dplyr r-fpc r-ggplot2 r-igraph r-maaslin2 r-metafor r-stringr r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MMUPHin") (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") (description "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: @itemize @item covariate-controlled batch- and cohort effect adjustment; @item meta-analysis differential abundance testing; @item meta-analysis unsupervised discrete structure (clustering) discovery; @item meta-analysis unsupervised continuous structure discovery. @end itemize") (license license:expat))) (define-public r-motifrg (package (name "r-motifrg") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-iranges r-seqlogo r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description "This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) (define-public r-muscat (package (name "r-muscat") (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 "061dgs3ygvr4vrc6mrmikqn4a7a5qajn7k8crbskdkg4svg8qv1a")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-blme r-complexheatmap r-data-table r-deseq2 r-dplyr r-edger r-ggplot2 r-glmmtmb r-limma r-lme4 r-lmertest r-matrix r-matrixstats r-progress r-purrr r-s4vectors r-scales r-scater r-sctransform r-scuttle r-singlecellexperiment r-summarizedexperiment r-variancepartition r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/HelenaLC/muscat") (synopsis "Multi-sample multi-group scRNA-seq data analysis tools") (description "This package @code{muscat} provides various methods and visualization tools for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.") (license license:gpl3))) (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") (version "3.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 "0d0fsc4x8psfd93asi2d5kq1888s963d3s8kcihd5knqah000mh8")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome ;; These two packages are suggested packages r-bsgenome-hsapiens-1000genomes-hs37d5 r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-dplyr r-genomeinfodb r-genomicranges r-ggalluvial r-ggdendro r-ggplot2 r-iranges r-magrittr r-nmf r-pracma r-purrr r-rcolorbrewer r-s4vectors r-stringr r-tibble r-tidyr r-variantannotation)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.") (license license:expat))) (define-public r-msa (package (name "r-msa") (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 "064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-rcpp r-s4vectors)) (native-inputs (list r-knitr)) (home-page "http://www.bioinf.jku.at/software/msa/") (synopsis "Multiple sequence alignment") (description "The msa package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.") (license license:gpl2+))) (define-public r-msnbase (package (name "r-msnbase") (version "2.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-biocgenerics r-biocparallel r-digest r-ggplot2 r-impute r-iranges r-lattice r-maldiquant r-mass r-mscoreutils r-mzid r-mzr r-pcamethods r-plyr r-protgenerics r-rcpp r-s4vectors r-scales r-vsn r-xml)) (native-inputs (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description "This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.") (license license:artistic2.0))) (define-public r-msnid (package (name "r-msnid") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-annotationdbi r-annotationhub r-biobase r-biocgenerics r-biocstyle r-biostrings r-data-table r-doparallel r-dplyr r-foreach r-ggplot2 r-iterators r-msnbase r-msmstests r-mzid r-mzr r-protgenerics r-purrr r-r-cache r-rcpp r-reshape2 r-rlang r-runit r-stringr r-tibble r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) (define-public r-mzid (package (name "r-mzid") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-iterators r-plyr r-protgenerics r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description "This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) (define-public r-mzr (package (name "r-mzr") (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "mzR"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-boost (lambda _ (substitute* "src/Makevars" (("\\./boost/libs.*") "") (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") (("\\ARCH_OBJS=" line) (string-append line "\nBOOST_LIBS=-lboost_system -lboost_regex \ -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))))))) (inputs (list boost ; use this instead of the bundled boost sources zlib)) (propagated-inputs (list r-biobase r-biocgenerics r-ncdf4 r-protgenerics r-rcpp r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description "The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-numbat (package (name "r-numbat") (version "1.2.2") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 "06qq7i8k1mi7yg1irfbk3d2fmk7awvzj7h7r54hnr6pzywk7nmhc")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape r-catools r-data-table r-dendextend r-dplyr r-genomicranges r-ggplot2 r-ggraph r-ggtree r-glue r-igraph r-iranges r-logger r-magrittr r-matrix r-optparse r-paralleldist r-patchwork r-pryr r-purrr r-r-utils r-rcpp r-rcpparmadillo r-rhpcblasctl r-roptim r-scales r-scistreer r-stringr r-tibble r-tidygraph r-tidyr r-vcfr r-zoo)) (home-page "https://github.com/kharchenkolab/numbat") (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") (description "This package provides a computational method that infers copy number variations (CNV) in cancer scRNA-seq data and reconstructs the tumor phylogeny. It integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. It does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). It can be used to: @enumerate @item detect allele-specific copy number variations from single-cells @item differentiate tumor versus normal cells in the tumor microenvironment @item infer the clonal architecture and evolutionary history of profiled tumors @end enumerate For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, Gao et al in Nature Biotechnology 2022}.") (license license:expat))) (define-public r-organism-dplyr (package (name "r-organism-dplyr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationfilter r-biocfilecache r-dbi r-dbplyr r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-rlang r-rsqlite r-s4vectors r-tibble)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Organism.dplyr") (synopsis "Dplyr-based access to Bioconductor annotation resources") (description "This package provides an alternative interface to Bioconductor @code{ annotation} resources, in particular the gene identifier mapping functionality of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate functionality of the @code{TxDb} packages (e.g., @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).") (license license:artistic2.0))) (define-public r-organismdbi (package (name "r-organismdbi") (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biocmanager r-dbi r-genomicfeatures r-genomicranges r-graph r-iranges r-rbgl r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.") (license license:artistic2.0))) (define-public r-oscope (package (name "r-oscope") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) (home-page "https://bioconductor.org/packages/Oscope") (synopsis "Oscillatory genes identifier in unsynchronized single cell RNA-seq") (description "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. This statistical pipeline has been developed to identify and recover the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.") (license license:asl2.0))) (define-public r-pcaexplorer (package (name "r-pcaexplorer") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-base64enc r-biomart r-deseq2 r-dt r-genefilter r-genomicranges r-ggplot2 r-ggrepel r-go-db r-gostats r-heatmaply r-iranges r-knitr r-limma r-nmf r-pheatmap r-plotly r-plyr r-rmarkdown r-s4vectors r-scales r-shiny r-shinyace r-shinybs r-shinydashboard r-summarizedexperiment r-threejs r-tidyr r-topgo)) (native-inputs (list r-knitr)) (home-page "https://github.com/federicomarini/pcaExplorer") (synopsis "Interactive Visualization of RNA-seq Data Using a Principal Components Approach") (description "This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.") (license license:expat))) (define-public r-pcamethods (package (name "r-pcamethods") (version "1.90.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs (package (name "r-pscbs") (version "0.66.0") (source (origin (method url-fetch) (uri (cran-uri "PSCBS" version)) (sha256 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) (properties `((upstream-name . "PSCBS"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-aroma-light r-dnacopy r-future r-listenv r-matrixstats r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (native-inputs (list r-r-rsp ;used to build vignettes r-r-devices)) (home-page "https://github.com/HenrikBengtsson/PSCBS") (synopsis "Analysis of parent-specific DNA copy numbers") (description "This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (license license:gpl2+))) (define-public r-protgenerics (package (name "r-protgenerics") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") (synopsis "S4 generic functions for proteomics infrastructure") (description "This package provides S4 generic functions needed by Bioconductor proteomics packages.") (license license:artistic2.0))) (define-public r-rbgl (package (name "r-rbgl") (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs (list r-bh r-graph)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description "This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.") (license license:artistic2.0))) (define-public r-rcas (package (name "r-rcas") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-data-table r-dt r-genomation r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-ggseqlogo r-gprofiler2 r-iranges r-knitr r-pbapply r-pheatmap r-plotly r-plotrix r-proxy r-ranger r-rsqlite r-rtracklayer r-rmarkdown r-s4vectors pandoc)) (native-inputs (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.") (home-page "https://github.com/BIMSBbioinfo/RCAS") (license license:artistic2.0))) (define-public r-regioner (package (name "r-regioner") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-bsgenome r-genomeinfodb r-genomicranges r-iranges r-memoise r-rtracklayer r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.") (license license:artistic2.0))) (define-public r-reportingtools (package (name "r-reportingtools") (version "2.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs (list r-annotate r-annotationdbi r-biobase r-biocgenerics r-category r-deseq2 r-edger r-ggbio r-ggplot2 r-gostats r-gseabase r-hwriter r-iranges r-knitr r-lattice r-limma r-pfam-db r-r-utils r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description "The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) (define-public r-rhdf5 (package (name "r-rhdf5") (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 "1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description "This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.") (license license:artistic2.0))) (define-public r-rhdf5filters (package (name "r-rhdf5filters") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 "17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1")))) (properties `((upstream-name . 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(define-public r-restfulr (package (name "r-restfulr") (version "0.0.15") (source (origin (method url-fetch) (uri (cran-uri "restfulr" version)) (sha256 (base32 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0")))) (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description "This package models a RESTful service as if it were a nested R list.") 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The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-samr (package (name "r-samr") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "samr" version)) (sha256 (base32 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) (properties `((upstream-name . 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(define-public r-scistreer (package (name "r-scistreer") (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "scistreer" version)) (sha256 (base32 "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) (properties `((upstream-name . "scistreer"))) (build-system r-build-system) (propagated-inputs (list r-ape r-dplyr r-ggplot2 r-ggtree r-igraph r-paralleldist r-patchwork r-phangorn r-rcpp r-rcpparmadillo r-rcppparallel r-reshape2 r-rhpcblasctl r-stringr r-tidygraph)) (home-page "https://github.com/kharchenkolab/scistreer") (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") (description "This package provides fast maximum-likelihood phylogeny inference from noisy single-cell data using the ScisTree algorithm proposed by @code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the method applicable to massive single-cell datasets (>10,000 cells).") 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However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. @code{scmap} is a method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.") (license license:gpl3))) (define-public r-scry (package (name "r-scry") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) (properties `((upstream-name . 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The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events.") 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It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) ;; This is a CRAN package but it depends on a bioconductor package. (define-public r-speaq (package (name "r-speaq") (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "speaq" version)) (sha256 (base32 "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) (properties `((upstream-name . "speaq"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-data-table r-dosnow r-foreach r-ggplot2 r-gridextra r-impute r-massspecwavelet r-missforest r-reshape2 r-rfast r-rvest r-xml2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=speaq") (synopsis "Tools for nuclear magnetic resonance spectra alignment") (description "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy data analysis as easy as possible. 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(license license:lgpl2.1+))) (define-public r-tximport (package (name "r-tximport") (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description "This package provides tools to import transcript-level abundance, estimated counts and transcript lengths, and to summarize them into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package. 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An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") 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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 "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-rtsne r-slam)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "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. 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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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-ggplot2 r-ggrepel r-iranges r-limma r-qqman r-s4vectors r-summarizedexperiment)) (native-inputs (list 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. 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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).") 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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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-iranges r-readr r-regioner r-reshape2 r-rtracklayer r-s4vectors)) (native-inputs (list 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. 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(license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-data-table r-flowclust r-flowcore r-flowviz r-flowworkspace r-graph r-ncdfflow r-rbgl r-rcolorbrewer)) (native-inputs (list 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.") 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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 "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs (list r-arrow r-aucell r-biocgenerics r-data-table r-dplyr r-genomeinfodb r-genomicranges r-gseabase r-r-utils r-s4vectors r-summarizedexperiment r-tibble)) (native-inputs (list 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-chicago (package (name "r-chicago") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description "This package provides a pipeline for analysing Capture Hi-C data.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-ciara (package (name "r-ciara") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "CIARA" version)) (sha256 (base32 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-cicero (package (name "r-cicero") (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "1gf359x6lvm3kc4mlsh7vxf8lmvhp080fi0cksvb4mcypafp67cv")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-biobase r-biocgenerics r-data-table r-dplyr r-fnn r-genomicranges r-ggplot2 r-glasso r-gviz r-igraph r-iranges r-matrix r-monocle r-plyr r-reshape2 r-s4vectors r-stringi r-stringr r-tibble r-tidyr r-vgam)) (native-inputs (list 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 (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 "1i954hn7xyajpkg4fks04jd86flcmy2326nzpmxgy8h69jkzdc8q")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-cistopic (package (name "r-cistopic") (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs (list r-aucell r-data-table r-dplyr r-dosnow r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer 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-cistopic-next (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803") (revision "1")) (package (inherit r-cistopic) (name "r-cistopic-next") ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd ;; since the previous release is 2.1.0. Oh well. (version (git-version "0.3.0" 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 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-roc (package (name "r-roc") (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs (list 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-watermelon (package (name "r-watermelon") (version "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-illuminahumanmethylation450kanno-ilmn12-hg19 r-illuminaio r-limma r-lumi r-matrixstats r-methylumi r-roc)) (native-inputs (list r-knitr)) (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 "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06")) (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 ">"))))))) (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs (list lz4 xz zlib)) (native-inputs (list 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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-gdsfmt r-geoquery r-illuminaio r-methylumi r-minfi r-watermelon)) (native-inputs (list r-knitr)) (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 "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicranges 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-reqon (package (name "r-reqon") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs (list r-rjava r-rsamtools 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 "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) (properties `((upstream-name . 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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-tilingarray (package (name "r-tilingarray") (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) (properties `((upstream-name . 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The main functionalities of the package are: @enumerate @item the class segmentation for representing partitionings of a linear series of data; @item the function segment for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; @item the function @code{confint} for calculating confidence intervals using the @code{strucchange} package; @item the function @code{plotAlongChrom} for generating pretty plots; @item the function @code{normalizeByReference} for probe-sequence dependent response adjustment from a (set of) reference hybridizations. @end enumerate") (license license:artistic2.0))) (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c")))) (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 (list r-affy r-biobase r-biostrings r-genomegraphs r-genomicranges r-iranges r-oligo r-oligoclasses r-preprocesscore 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.") 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(license license:gpl2))) (define-public r-omnipathr (package (name "r-omnipathr") (version "3.5.25") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-checkmate r-crayon r-curl r-digest r-dplyr r-httr r-igraph r-jsonlite r-later r-logger r-magrittr r-rmarkdown r-progress r-purrr r-rappdirs r-readr r-readxl r-rlang r-rvest r-stringr r-tibble r-tidyr r-tidyselect r-withr r-xml2 r-yaml)) (native-inputs (list r-knitr)) (home-page "https://saezlab.github.io/OmnipathR/") (synopsis "OmniPath web service client and more") (description "This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.") (license license:expat))) (define-public r-biscuiteer (package (name "r-biscuiteer") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel r-biscuiteerdata r-bsseq r-data-table r-delayedmatrixstats r-dmrseq r-genomeinfodb r-genomicranges r-gtools r-hdf5array r-homo-sapiens r-impute r-iranges r-matrix r-matrixstats r-mus-musculus r-qdnaseq r-qualv r-r-utils r-readr r-rsamtools r-rtracklayer r-s4vectors r-summarizedexperiment r-variantannotation)) (native-inputs (list r-knitr)) (home-page "https://github.com/trichelab/biscuiteer") (synopsis "Convenience functions for the Biscuit package") (description "This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.") (license license:gpl3))) (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") (version "2.25.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs (list r-biomart r-data-table r-downloader r-dplyr r-genomicranges r-ggplot2 r-httr r-iranges r-jsonlite r-knitr r-plyr r-purrr r-r-utils r-readr r-rvest r-s4vectors r-stringr r-summarizedexperiment r-tcgabiolinksgui-data r-tibble r-tidyr r-xml r-xml2)) (native-inputs (list r-knitr)) (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks") (synopsis "Integrative analysis with GDC data") (description "The aim of TCGAbiolinks is: @enumerate @item facilitate GDC open-access data retrieval; @item prepare the data using the appropriate pre-processing strategies; @item provide the means to carry out different standard analyses, and; @item to easily reproduce earlier research results. @end enumerate In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.") (license license:gpl3+))) (define-public r-tricycle (package (name "r-tricycle") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-circular r-dplyr r-genomicranges r-ggnewscale r-ggplot2 r-iranges r-rcolorbrewer r-s4vectors r-scater r-scattermore r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hansenlab/tricycle") (synopsis "Transferable representation and inference of cell cycle") (description "The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The @code{tricycle} provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.") (license license:gpl3))) (define-public r-tximeta (package (name "r-tximeta") (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 "15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-biocfilecache r-biostrings r-ensembldb r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-jsonlite r-matrix r-s4vectors r-summarizedexperiment r-tibble r-tximport)) (native-inputs (list r-knitr)) (home-page "https://github.com/mikelove/tximeta") (synopsis "Transcript quantification import with automatic metadata") (description "This package implements transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.") (license license:gpl2))) (define-public r-phyloseq (package (name "r-phyloseq") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-biobase r-biocgenerics r-biomformat r-biostrings r-cluster r-data-table r-foreach r-ggplot2 r-igraph r-multtest r-plyr r-reshape2 r-scales r-vegan)) (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description "Phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.") (license license:agpl3))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;