;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 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 ;;; Copyright © 2021 Hong Li ;;; ;;; 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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All classes in the package use consistent naming and share the same rich and consistent \"Vector API\" as much as possible.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package (name "r-absfiltergsea") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "AbsFilterGSEA" version)) (sha256 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) (properties `((upstream-name . 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"BisqueRNA"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limsolve" ,r-limsolve))) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.") (license license:gpl3))) ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs (package (name "r-deconstructsigs") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "deconstructSigs" version)) (sha256 (base32 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) (properties `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomeinfodb" ,r-genomeinfodb) ("r-reshape2" ,r-reshape2))) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package (name "r-nmf") (version "0.23.0") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g")))) (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-annotationdbi (package (name "r-annotationdbi") (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-iranges" ,r-iranges) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationDbi") (synopsis "Annotation database interface") (description "This package provides user interface and database connection code for annotation data packages using SQLite data storage.") (license license:artistic2.0))) (define-public r-annotationforge (package (name "r-annotationforge") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/AnnotationForge") (synopsis "Code for building annotation database packages") (description "This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) (define-public r-biobase (package (name "r-biobase") (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description "This package provides functions that are needed by many other packages on Bioconductor or which replace R functions.") (license license:artistic2.0))) (define-public r-biomart (package (name "r-biomart") (version "2.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) (properties `((upstream-name . 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These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.") (license license:artistic2.0))) (define-public r-biocparallel (package (name "r-biocparallel") (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ ;; Remove generated documentation. (for-each delete-file '("inst/doc/BiocParallel_BatchtoolsParam.pdf" "inst/doc/Introduction_To_BiocParallel.pdf" "inst/doc/Errors_Logs_And_Debugging.pdf" "inst/doc/BiocParallel_BatchtoolsParam.R" "inst/doc/Introduction_To_BiocParallel.R" "inst/doc/Errors_Logs_And_Debugging.R")) ;; Remove time-dependent macro (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" "inst/doc/Introduction_To_BiocParallel.Rnw" "inst/doc/Errors_Logs_And_Debugging.Rnw" "vignettes/BiocParallel_BatchtoolsParam.Rnw" "vignettes/Introduction_To_BiocParallel.Rnw" "vignettes/Errors_Logs_And_Debugging.Rnw") (("\\today") "later")) ;; Initialize the random number generator seed when building. 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"Biostrings"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-crayon" ,r-crayon) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) (home-page "https://bioconductor.org/packages/Biostrings") (synopsis "String objects and algorithms for biological sequences") (description "This package provides memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.") (license license:artistic2.0))) (define-public r-category (package (name "r-category") (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-genefilter" ,r-genefilter) ("r-graph" ,r-graph) ("r-gseabase" ,r-gseabase) ("r-matrix" ,r-matrix) ("r-rbgl" ,r-rbgl) ("r-dbi" ,r-dbi))) (home-page "https://bioconductor.org/packages/Category") (synopsis "Category analysis") (description "This package provides a collection of tools for performing category analysis.") (license license:artistic2.0))) (define-public r-deseq2 (package (name "r-deseq2") (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19")))) (properties `((upstream-name . 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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 . 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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 . 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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 "3.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 "0l417aygs89wf1j9fjpfjhahzskbpbgcrm8xpx3qm4s0307vfzkw")))) (properties `((upstream-name . 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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.") 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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.") 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It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) (define-public r-monocle3 (package (name "r-monocle3") (version "0.1.2") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/monocle3") (commit version))) (file-name (git-file-name name version)) (sha256 (base32 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-grr" ,r-grr) ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-limma" ,r-limma) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-matrix-utils" ,r-matrix-utils) ("r-pbapply" ,r-pbapply) ("r-pbmcapply" ,r-pbmcapply) ("r-pheatmap" ,r-pheatmap) ("r-plotly" ,r-plotly) ("r-pryr" ,r-pryr) ("r-proxy" ,r-proxy) ("r-pscl" ,r-pscl) ("r-purrr" ,r-purrr) ("r-rann" ,r-rann) ("r-rcpp" ,r-rcpp) ("r-rcppparallel" ,r-rcppparallel) ("r-reshape2" ,r-reshape2) ("r-reticulate" ,r-reticulate) ("r-rhpcblasctl" ,r-rhpcblasctl) ("r-rtsne" ,r-rtsne) ("r-shiny" ,r-shiny) ("r-slam" ,r-slam) ("r-spdep" ,r-spdep) ("r-speedglm" ,r-speedglm) ("r-stringr" ,r-stringr) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-uwot" ,r-uwot) ("r-viridis" ,r-viridis))) (home-page "https://github.com/cole-trapnell-lab/monocle3") (synopsis "Analysis toolkit for single-cell RNA-Seq data") (description "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") (license license:expat))) (define-public r-noiseq (package (name "r-noiseq") (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/NOISeq") (synopsis "Exploratory analysis and differential expression for RNA-seq data") (description "This package provides tools to support the analysis of RNA-seq expression data or other similar kind of data. It provides exploratory plots to evaluate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. It also supports the analysis of differential expression between two experimental conditions with no parametric assumptions.") (license license:artistic2.0))) (define-public r-scdd (package (name "r-scdd") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs `(("r-arm" ,r-arm) ("r-biocparallel" ,r-biocparallel) ("r-ebseq" ,r-ebseq) ("r-fields" ,r-fields) ("r-ggplot2" ,r-ggplot2) ("r-mclust" ,r-mclust) ("r-outliers" ,r-outliers) ("r-s4vectors" ,r-s4vectors) ("r-scran" ,r-scran) ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/kdkorthauer/scDD") (synopsis "Mixture modeling of single-cell RNA-seq data") (description "This package implements a method to analyze single-cell RNA-seq data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.") (license license:gpl2))) (define-public r-scone (package (name "r-scone") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) ("r-biocparallel" ,r-biocparallel) ("r-boot" ,r-boot) ("r-class" ,r-class) ("r-cluster" ,r-cluster) ("r-compositions" ,r-compositions) ("r-diptest" ,r-diptest) ("r-edger" ,r-edger) ("r-fpc" ,r-fpc) ("r-gplots" ,r-gplots) ("r-hexbin" ,r-hexbin) ("r-limma" ,r-limma) ("r-matrixstats" ,r-matrixstats) ("r-mixtools" ,r-mixtools) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rhdf5" ,r-rhdf5) ("r-ruvseq" ,r-ruvseq) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/scone") (synopsis "Single cell overview of normalized expression data") (description "SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.") (license license:artistic2.0))) (define-public r-geoquery (package (name "r-geoquery") (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-readr" ,r-readr) ("r-tidyr" ,r-tidyr) ("r-xml2" ,r-xml2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/seandavi/GEOquery/") (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") (description "The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.") (license license:gpl2))) (define-public r-illuminaio (package (name "r-illuminaio") (version "0.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay")))) (build-system r-build-system) (propagated-inputs `(("r-base64" ,r-base64))) (home-page "https://github.com/HenrikBengtsson/illuminaio/") (synopsis "Parse Illumina microarray output files") (description "This package provides tools for parsing Illumina's microarray output files, including IDAT.") (license license:gpl2))) (define-public r-siggenes (package (name "r-siggenes") (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-multtest" ,r-multtest) ("r-scrime" ,r-scrime))) (home-page "https://bioconductor.org/packages/siggenes/") (synopsis "Multiple testing using SAM and Efron's empirical Bayes approaches") (description "This package provides tools for the identification of differentially expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical Bayes Analyses of Microarrays} (EBAM).") (license license:lgpl2.0+))) (define-public r-bumphunter (package (name "r-bumphunter") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-dorng" ,r-dorng) ("r-foreach" ,r-foreach) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-iterators" ,r-iterators) ("r-limma" ,r-limma) ("r-locfit" ,r-locfit) ("r-matrixstats" ,r-matrixstats) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/ririzarr/bumphunter") (synopsis "Find bumps in genomic data") (description "This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.") (license license:artistic2.0))) (define-public r-minfi (package (name "r-minfi") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi")))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bumphunter" ,r-bumphunter) ("r-data-table" ,r-data-table) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-geoquery" ,r-geoquery) ("r-hdf5array" ,r-hdf5array) ("r-illuminaio" ,r-illuminaio) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-limma" ,r-limma) ("r-mass" ,r-mass) ("r-mclust" ,r-mclust) ("r-nlme" ,r-nlme) ("r-nor1mix" ,r-nor1mix) ("r-preprocesscore" ,r-preprocesscore) ("r-quadprog" ,r-quadprog) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape" ,r-reshape) ("r-s4vectors" ,r-s4vectors) ("r-siggenes" ,r-siggenes) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/hansenlab/minfi") (synopsis "Analyze Illumina Infinium DNA methylation arrays") (description "This package provides tools to analyze and visualize Illumina Infinium methylation arrays.") (license license:artistic2.0))) (define-public r-methylumi (package (name "r-methylumi") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) ("r-genefilter" ,r-genefilter) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-illuminaio" ,r-illuminaio) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-matrixstats" ,r-matrixstats) ("r-minfi" ,r-minfi) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-scales" ,r-scales) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/methylumi") (synopsis "Handle Illumina methylation data") (description "This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. 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.") (license license:gpl2))) (define-public r-lumi (package (name "r-lumi") (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-dbi" ,r-dbi) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-kernsmooth" ,r-kernsmooth) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-methylumi" ,r-methylumi) ("r-mgcv" ,r-mgcv) ("r-nleqslv" ,r-nleqslv) ("r-preprocesscore" ,r-preprocesscore) ("r-rsqlite" ,r-rsqlite))) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.") (license license:lgpl2.0+))) (define-public r-linnorm (package (name "r-linnorm") (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs `(("r-amap" ,r-amap) ("r-apcluster" ,r-apcluster) ("r-ellipse" ,r-ellipse) ("r-fastcluster" ,r-fastcluster) ("r-fpc" ,r-fpc) ("r-ggdendro" ,r-ggdendro) ("r-ggplot2" ,r-ggplot2) ("r-gmodels" ,r-gmodels) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) ("r-mass" ,r-mass) ("r-mclust" ,r-mclust) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rtsne" ,r-rtsne) ("r-statmod" ,r-statmod) ("r-vegan" ,r-vegan) ("r-zoo" ,r-zoo))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function (@code{Linnorm}), the following pipelines are implemented: @enumerate @item Library size/batch effect normalization (@code{Linnorm.Norm}) @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or hierarchical clustering (@code{Linnorm.tSNE}, @code{Linnorm.PCA}, @code{Linnorm.HClust}) @item Differential expression analysis or differential peak detection using limma (@code{Linnorm.limma}) @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) @item Stable gene selection for scRNA-seq data; for users without or who do not want to rely on spike-in genes (@code{Linnorm.SGenes}) @item Data imputation (@code{Linnorm.DataImput}). @end enumerate Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the @code{RnaXSim} function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.") (license license:expat))) (define-public r-ioniser (package (name "r-ioniser") (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) ("r-biostrings" ,r-biostrings) ("r-bit64" ,r-bit64) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-magrittr" ,r-magrittr) ("r-rhdf5" ,r-rhdf5) ("r-shortread" ,r-shortread) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-xvector" ,r-xvector))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description "IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) ;; This is a CRAN package, but it depends on 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.") (license license:gpl2))) (define-public r-triform (package (name "r-triform") (version "1.29.0") (source (origin (method url-fetch) (uri (bioconductor-uri "triform" version)) (sha256 (base32 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-iranges" ,r-iranges) ("r-yaml" ,r-yaml))) (home-page "https://bioconductor.org/packages/triform/") (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") (description "The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.") (license license:gpl2))) (define-public r-varianttools (package (name "r-varianttools") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89")))) (properties `((upstream-name . 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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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"GenomicScores"))) (build-system r-build-system) (propagated-inputs `(("r-annotationhub" ,r-annotationhub) ("r-biobase" ,r-biobase) ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-delayedarray" ,r-delayedarray) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-hdf5array" ,r-hdf5array) ("r-iranges" ,r-iranges) ("r-rhdf5" ,r-rhdf5) ("r-s4vectors" ,r-s4vectors) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/rcastelo/GenomicScores/") (synopsis "Work with genome-wide position-specific scores") (description "This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.") (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 . "GOfuncR"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-genomicranges" ,r-genomicranges) ("r-gtools" ,r-gtools) ("r-iranges" ,r-iranges) ("r-mapplots" ,r-mapplots) ("r-rcpp" ,r-rcpp) ("r-vioplot" ,r-vioplot))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/GOfuncR/") (synopsis "Gene ontology enrichment using FUNC") (description "GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is included in the package and updated regularly. 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 . "AllelicImbalance"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-gridextra" ,r-gridextra) ("r-gviz" ,r-gviz) ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-nlme" ,r-nlme) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/pappewaio/AllelicImbalance") (synopsis "Investigate allele-specific expression") (description "This package provides a framework for allele-specific expression investigation using RNA-seq data.") (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 . "EBImage"))) (build-system r-build-system) (propagated-inputs `(("r-abind" ,r-abind) ("r-biocgenerics" ,r-biocgenerics) ("r-fftwtools" ,r-fftwtools) ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-jpeg" ,r-jpeg) ("r-locfit" ,r-locfit) ("r-png" ,r-png) ("r-rcurl" ,r-rcurl) ("r-tiff" ,r-tiff))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://github.com/aoles/EBImage") (synopsis "Image processing and analysis toolbox for R") (description "EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.") ;; Any version of the LGPL. (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. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures and a signature analysis on @dfn{stratified mutational catalogue} (SMC) are provided.") (license license:gpl3))) (define-public r-gcrma (package (name "r-gcrma") (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-affyio" ,r-affyio) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-biostrings" ,r-biostrings) ("r-xvector" ,r-xvector))) (home-page "https://bioconductor.org/packages/gcrma/") (synopsis "Background adjustment using sequence information") (description "Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and @dfn{non-specific binding} (NSB). 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. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific binding is expected.") ;; Any version of the LGPL (license license:lgpl2.1+))) (define-public r-simpleaffy (package (name "r-simpleaffy") (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simpleaffy" version)) (sha256 (base32 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-gcrma" ,r-gcrma) ("r-genefilter" ,r-genefilter))) (home-page "https://bioconductor.org/packages/simpleaffy/") (synopsis "Very simple high level analysis of Affymetrix data") (description "This package provides high level functions for reading Affy @file{.CEL} files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the @code{affy} library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.") (license license:gpl2+))) (define-public r-yaqcaffy (package (name "r-yaqcaffy") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yaqcaffy" version)) (sha256 (base32 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96")))) (build-system r-build-system) (propagated-inputs `(("r-simpleaffy" ,r-simpleaffy))) (home-page "https://bioconductor.org/packages/yaqcaffy/") (synopsis "Affymetrix quality control and reproducibility analysis") (description "This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.") (license license:artistic2.0))) (define-public r-quantro (package (name "r-quantro") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-iterators" ,r-iterators) ("r-minfi" ,r-minfi) ("r-rcolorbrewer" ,r-rcolorbrewer))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/quantro/") (synopsis "Test for when to use quantile normalization") (description "This package provides a data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). 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. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.") (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.") (license license:gpl3))) (define-public r-xbseq (package (name "r-xbseq") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-locfit" ,r-locfit) ("r-magrittr" ,r-magrittr) ("r-matrixstats" ,r-matrixstats) ("r-pracma" ,r-pracma) ("r-roar" ,r-roar))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential expression} (DE), where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. 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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 . 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(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 "2.4.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "0c4akc89p5467n5rzq9bi7h0h15rbpqpvh7fw42qcj7g2vc41wba")))) (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 "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1")))) (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) ("zlib" ,zlib))) (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 combining and analyzing 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 . "TimeSeriesExperiment"))) (build-system r-build-system) (propagated-inputs `(("r-deseq2" ,r-deseq2) ("r-dplyr" ,r-dplyr) ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) ("r-ggplot2" ,r-ggplot2) ("r-hmisc" ,r-hmisc) ("r-limma" ,r-limma) ("r-magrittr" ,r-magrittr) ("r-proxy" ,r-proxy) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vegan" ,r-vegan) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") (synopsis "Analysis for short time-series data") (description "This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.") (license license:lgpl3+))) (define-public r-variantfiltering (package (name "r-variantfiltering") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5")))) (properties `((upstream-name . 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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 . 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(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. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias.") (license license:gpl3))) (define-public r-rsbml (package (name "r-rsbml") (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs `(("libsbml" ,libsbml) ("zlib" ,zlib))) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-graph" ,r-graph))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "http://www.sbml.org") (synopsis "R support for SBML") (description "This package provides an R interface to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") 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It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.") (license license:gpl3))) (define-public r-chemminer (package (name "r-chemminer") (version "3.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) ("r-biocgenerics" ,r-biocgenerics) ("r-dbi" ,r-dbi) ("r-digest" ,r-digest) ("r-dt" ,r-dt) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-png" ,r-png) ("r-rcpp" ,r-rcpp) ("r-rcurl" ,r-rcurl) ("r-rjson" ,r-rjson) ("r-rsvg" ,r-rsvg))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/girke-lab/ChemmineR") (synopsis "Cheminformatics toolkit for R") (description "ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.") (license license:artistic2.0))) (define-public r-bioassayr (package (name "r-bioassayr") (version "1.28.3") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 "03pdb76j7c28b1h1flb40ahq7i9iha22kblq6mkl3x4xmrdgaw5y")))) (properties `((upstream-name . 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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))) ;; This is a CRAN package, but it depends on r-rgraphviz, which is a ;; Bioconductor package. (define-public r-abn (package (name "r-abn") (version "2.5-0") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw")))) (build-system r-build-system) (inputs `(("gsl" ,gsl))) (propagated-inputs `(("r-lme4" ,r-lme4) ("r-nnet" ,r-nnet) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rgraphviz" ,r-rgraphviz) ("r-rjags" ,r-rjags))) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description "Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a @dfn{generalized linear model} (GLM). Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. This package provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.") (license license:gpl2+))) (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-chromstar (package (name "r-chromstar") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs `(("r-bamsignals" ,r-bamsignals) ("r-biocgenerics" ,r-biocgenerics) ("r-chromstardata" ,r-chromstardata) ("r-doparallel" ,r-doparallel) ("r-foreach" ,r-foreach) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-mvtnorm" ,r-mvtnorm) ("r-reshape2" ,r-reshape2) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ataudt/chromstaR") (synopsis "Chromatin state analysis for ChIP-Seq data") (description "This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.") (license license:artistic2.0))) (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 . "Sushi"))) (build-system r-build-system) (propagated-inputs `(("r-biomart" ,r-biomart) ("r-zoo" ,r-zoo))) (home-page "https://bioconductor.org/packages/Sushi") (synopsis "Tools for visualizing genomics data") (description "This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.") (license license:gpl2+)))