;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) (properties `((upstream-name . 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(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.") 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Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.") 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(license license:lgpl2.0+))) (define-public r-qvalue (package (name "r-qvalue") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/StoreyLab/qvalue") (synopsis "Q-value estimation for false discovery rate control") (description "This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local @dfn{false discovery rate} (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) (define r-rcppnumerical (package (name "r-rcppnumerical") (version "0.4-0") (source (origin (method url-fetch) (uri (cran-uri "RcppNumerical" version)) (sha256 (base32 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik")))) (properties `((upstream-name . "RcppNumerical"))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis "Rcpp integration for numerical computing libraries") (description "This package provides a collection of open source libraries for numerical computing (numerical integration, optimization, etc.) and their integration with @code{Rcpp}.") (license license:gpl2+))) (define-public r-apeglm (package (name "r-apeglm") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs `(("r-emdbook" ,r-emdbook) ("r-genomicranges" ,r-genomicranges) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppnumerical" ,r-rcppnumerical) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.") (license license:gpl2))) (define-public r-greylistchip (package (name "r-greylistchip") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs `(("r-bsgenome" ,r-bsgenome) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-mass" ,r-mass) ("r-rsamtools" ,r-rsamtools) ("r-rtracklayer" ,r-rtracklayer) ("r-summarizedexperiment" ,r-summarizedexperiment))) (home-page "https://bioconductor.org/packages/GreyListChIP") (synopsis "Greylist artefact regions based on ChIP inputs") (description "This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling.") (license license:artistic2.0))) (define-public r-diffbind (package (name "r-diffbind") (version "3.0.8") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) (properties `((upstream-name . 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Also enables occupancy (overlap) analysis and plotting functions.") (license license:artistic2.0))) (define-public r-ripseeker (package (name "r-ripseeker") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomicranges" ,r-genomicranges) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-rsamtools" ,r-rsamtools) ("r-genomicalignments" ,r-genomicalignments) ("r-rtracklayer" ,r-rtracklayer))) (home-page "https://bioconductor.org/packages/RIPSeeker") (synopsis "Identifying protein-associated transcripts from RIP-seq experiments") (description "This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) (define-public r-multtest (package (name "r-multtest") (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q")))) (build-system r-build-system) (propagated-inputs `(("r-survival" ,r-survival) ("r-biocgenerics" ,r-biocgenerics) ("r-biobase" ,r-biobase) ("r-mass" ,r-mass))) (home-page "https://bioconductor.org/packages/multtest") (synopsis "Resampling-based multiple hypothesis testing") (description "This package can do non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of T- and F-statistics (including T-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with T-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted P-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.") (license license:lgpl3))) (define-public r-graph (package (name "r-graph") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-ggm (package (name "r-ggm") (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "ggm" version)) (sha256 (base32 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) (properties `((upstream-name . "ggm"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-igraph" ,r-igraph))) (home-page "https://cran.r-project.org/package=ggm") (synopsis "Functions for graphical Markov models") (description "This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. (define-public r-perfmeas (package (name "r-perfmeas") (version "1.2.1") (source (origin (method url-fetch) (uri (cran-uri "PerfMeas" version)) (sha256 (base32 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93")))) (properties `((upstream-name . "PerfMeas"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph) ("r-limma" ,r-limma) ("r-rbgl" ,r-rbgl))) (home-page "https://cran.r-project.org/web/packages/PerfMeas/") (synopsis "Performance measures for ranking and classification tasks") (description "This package implements different performance measures for classification and ranking tasks. @dfn{Area under curve} (AUC), precision at a given recall, F-score for single and multiple classes are available.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-codedepends (package (name "r-codedepends") (version "0.6.5") (source (origin (method url-fetch) (uri (cran-uri "CodeDepends" version)) (sha256 (base32 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) (properties `((upstream-name . "CodeDepends"))) (build-system r-build-system) (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) ("r-xml" ,r-xml))) (home-page "https://cran.r-project.org/web/packages/CodeDepends") (synopsis "Analysis of R code for reproducible research and code comprehension") (description "This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-chippeakanno (package (name "r-chippeakanno") (version "3.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj")))) (properties `((upstream-name . 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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 "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) (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. 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(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.") 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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 . 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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 . 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(license license:expat))) ;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-gkmsvm (package (name "r-gkmsvm") (version "0.81.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs `(("r-kernlab" ,r-kernlab) ("r-rcpp" ,r-rcpp) ("r-rocr" ,r-rocr) ("r-seqinr" ,r-seqinr))) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") (description "This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package (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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The user is expected to have already aligned the reads with a separate tool, e.g., GSNAP via gmapR.") (license license:artistic2.0))) (define-public r-heatplus (package (name "r-heatplus") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs `(("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page "https://github.com/alexploner/Heatplus") (synopsis "Heatmaps with row and/or column covariates and colored clusters") (description "This package provides tools to display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.") (license license:gpl2+))) (define-public r-gosemsim (package (name "r-gosemsim") (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-go-db" ,r-go-db) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/GOSemSim") (synopsis "GO-terms semantic similarity measures") (description "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.") (license license:artistic2.0))) (define-public r-anota (package (name "r-anota") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x")))) (build-system r-build-system) (propagated-inputs `(("r-multtest" ,r-multtest) ("r-qvalue" ,r-qvalue))) (home-page "https://bioconductor.org/packages/anota/") (synopsis "Analysis of translational activity") (description "Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) (define-public r-sigpathway (package (name "r-sigpathway") (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-fgsea (package (name "r-fgsea") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n")))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biocparallel" ,r-biocparallel) ("r-data-table" ,r-data-table) ("r-fastmatch" ,r-fastmatch) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-matrix" ,r-matrix) ("r-rcpp" ,r-rcpp))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ctlab/fgsea/") (synopsis "Fast gene set enrichment analysis") (description "The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.") (license license:expat))) (define-public r-dose (package (name "r-dose") (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biocparallel" ,r-biocparallel) ("r-do-db" ,r-do-db) ("r-fgsea" ,r-fgsea) ("r-ggplot2" ,r-ggplot2) ("r-gosemsim" ,r-gosemsim) ("r-qvalue" ,r-qvalue) ("r-reshape2" ,r-reshape2))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://guangchuangyu.github.io/software/DOSE/") (synopsis "Disease ontology semantic and enrichment analysis") (description "This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang, respectively, for measuring semantic similarities among @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.") (license license:artistic2.0))) (define-public r-enrichplot (package (name "r-enrichplot") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) ("r-dose" ,r-dose) ("r-ggplot2" ,r-ggplot2) ("r-ggraph" ,r-ggraph) ("r-gosemsim" ,r-gosemsim) ("r-igraph" ,r-igraph) ("r-magrittr" ,r-magrittr) ("r-plyr" ,r-plyr) ("r-purrr" ,r-purrr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-scatterpie" ,r-scatterpie) ("r-shadowtext" ,r-shadowtext))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/GuangchuangYu/enrichplot") (synopsis "Visualization of functional enrichment result") (description "The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. 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(license license:artistic2.0))) (define-public r-atacseqqc (package (name "r-atacseqqc") (version "1.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9")))) (properties `((upstream-name . 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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.") 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The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measurable observed signal and background noise from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.") (license license:gpl3+))) (define-public r-massspecwavelet (package (name "r-massspecwavelet") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-wiggleplotr (package (name "r-wiggleplotr") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-cowplot" ,r-cowplot) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-purrr" ,r-purrr) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/wiggleplotr/") (synopsis "Make read coverage plots from BigWig files") (description "This package provides tools to visualize read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualization of exonic read coverage.") (license license:asl2.0))) (define-public r-widgettools (package (name "r-widgettools") (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") (synopsis "Tools for creating interactive tcltk widgets") (description "This package contains tools to support the construction of tcltk widgets in R.") ;; Any version of the LGPL. (license license:lgpl3+))) (define-public r-webbioc (package (name "r-webbioc") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj")))) (build-system r-build-system) (inputs `(("netpbm" ,netpbm) ("perl" ,perl))) (propagated-inputs `(("r-affy" ,r-affy) ("r-annaffy" ,r-annaffy) ("r-biobase" ,r-biobase) ("r-biocmanager" ,r-biocmanager) ("r-gcrma" ,r-gcrma) ("r-multtest" ,r-multtest) ("r-qvalue" ,r-qvalue) ("r-vsn" ,r-vsn))) (home-page "https://www.bioconductor.org/") (synopsis "Bioconductor web interface") (description "This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.") (license license:gpl2+))) (define-public r-zfpkm (package (name "r-zfpkm") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs `(("r-checkmate" ,r-checkmate) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/ronammar/zFPKM/") (synopsis "Functions to facilitate zFPKM transformations") (description "This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).") (license license:gpl3))) (define-public r-rbowtie2 (package (name "r-rbowtie2") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie2/") (synopsis "R wrapper for Bowtie2 and AdapterRemoval") (description "This package provides an R wrapper of the popular @code{bowtie2} sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for rapid adapter trimming, identification, and read merging.") (license license:gpl3+))) (define-public r-progeny (package (name "r-progeny") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gridextra" ,r-gridextra) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/saezlab/progeny") (synopsis "Pathway responsive gene activity inference") (description "This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication \"Perturbation-response genes reveal signaling footprints in cancer gene expression\".") (license license:asl2.0))) (define-public r-arrmnormalization (package (name "r-arrmnormalization") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) (home-page "https://bioconductor.org/packages/ARRmNormalization/") (synopsis "Adaptive robust regression normalization for methylation data") (description "This is a package to perform the @dfn{Adaptive Robust Regression method} (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.") (license license:artistic2.0))) (define-public r-biocfilecache (package (name "r-biocfilecache") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs `(("r-curl" ,r-curl) ("r-dbi" ,r-dbi) ("r-dbplyr" ,r-dbplyr) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) ("r-rappdirs" ,r-rappdirs) ("r-rsqlite" ,r-rsqlite))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/BiocFileCache/") (synopsis "Manage files across sessions") (description "This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.") (license license:artistic2.0))) (define-public r-iclusterplus (package (name "r-iclusterplus") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (home-page "https://bioconductor.org/packages/iClusterPlus/") (synopsis "Integrative clustering of multi-type genomic data") (description "iClusterPlus is developed for integrative clustering analysis of multi-type genomic data and is an enhanced version of iCluster proposed and developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise from the experiments where biological samples (e.g. tumor samples) are analyzed by multiple techniques, for instance, @dfn{array comparative genomic hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so on. In the iClusterPlus model, binary observations such as somatic mutation are modeled as Binomial processes; categorical observations such as copy number states are realizations of Multinomial random variables; counts are modeled as Poisson random processes; and continuous measures are modeled by Gaussian distributions.") (license license:gpl2+))) (define-public r-rbowtie (package (name "r-rbowtie") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/Rbowtie/") (synopsis "R bowtie wrapper") (description "This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool.") 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Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.") (license license:artistic2.0))) (define-public r-rhisat2 (package (name "r-rhisat2") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'make-reproducible (lambda _ (substitute* "src/Makefile" (("`hostname`") "guix") (("`date`") "0") ;; Avoid shelling out to "which". (("^CC =.*") (which "gcc")) (("^CPP =.*") (which "g++"))) #t))))) (propagated-inputs `(("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-sgseq" ,r-sgseq))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/fmicompbio/Rhisat2") (synopsis "R Wrapper for HISAT2 sequence aligner") (description "This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.") (license license:gpl3))) (define-public r-quasr (package (name "r-quasr") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8")))) (properties `((upstream-name . 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It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.") (license license:gpl2))) (define-public r-rqc (package (name "r-rqc") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-birewire (package (name "r-birewire") (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs `(("r-igraph" ,r-igraph) ("r-matrix" ,r-matrix) ("r-slam" ,r-slam) ("r-tsne" ,r-tsne))) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.") (license license:gpl3))) (define-public r-birta (package (name "r-birta") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-limma" ,r-limma) ("r-mass" ,r-mass))) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description "Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-iranges" ,r-iranges) ("r-limma" ,r-limma) ("r-qqman" ,r-qqman) ("r-s4vectors" ,r-s4vectors) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description "This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.") (license license:expat))) (define-public r-ropls (package (name "r-ropls") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-multidataset" ,r-multidataset))) (native-inputs `(("r-knitr" ,r-knitr))) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") (synopsis "Multivariate analysis and feature selection of omics data") (description "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. This package provides imlementations of PCA, PLS, and OPLS for multivariate analysis and feature selection of omics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients).") (license license:cecill))) (define-public r-biosigner (package (name "r-biosigner") (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-e1071" ,r-e1071) ("r-multidataset" ,r-multidataset) ("r-randomforest" ,r-randomforest) ("r-ropls" ,r-ropls))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description "Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationhub" ,r-annotationhub) ("r-dplyr" ,r-dplyr) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-iranges" ,r-iranges) ("r-readr" ,r-readr) ("r-regioner" ,r-regioner) ("r-reshape2" ,r-reshape2) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.") (license license:gpl3))) (define-public r-rsubread (package (name "r-rsubread") (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) (propagated-inputs `(("r-matrix" ,r-matrix))) (home-page "https://bioconductor.org/packages/Rsubread/") (synopsis "Subread sequence alignment and counting for R") (description "This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) (define-public r-flowutils (package (name "r-flowutils") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-flowcore" ,r-flowcore) ("r-graph" ,r-graph) ("r-runit" ,r-runit) ("r-xml" ,r-xml))) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description "This package provides utilities for flow cytometry data.") (license license:artistic2.0))) (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs `(("r-all" ,r-all) ("r-biobase" ,r-biobase) ("r-cluster" ,r-cluster))) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description "This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) (define-public r-cytolib (package (name "r-cytolib") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) (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. 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"flowCore"))) (build-system r-build-system) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-matrixstats" ,r-matrixstats) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rprotobuflib" ,r-rprotobuflib) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowCore") (synopsis "Basic structures for flow cytometry data") (description "This package provides S4 data structures and basic functions to deal with flow cytometry data.") (license license:artistic2.0))) (define-public r-flowmeans (package (name "r-flowmeans") (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-feature" ,r-feature) ("r-flowcore" ,r-flowcore) ("r-rrcov" ,r-rrcov))) (home-page "https://bioconductor.org/packages/flowMeans") (synopsis "Non-parametric flow cytometry data gating") (description "This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.") (license license:artistic2.0))) (define-public r-ncdfflow (package (name "r-ncdfflow") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\(RHDF5_LIBS\\)" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-flowcore" ,r-flowcore) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/ncdfFlow/") (synopsis "HDF5 based storage for flow cytometry data") (description "This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.") (license license:artistic2.0))) (define-public r-ggcyto (package (name "r-ggcyto") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs `(("r-data-table" ,r-data-table) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-hexbin" ,r-hexbin) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rlang" ,r-rlang) ("r-scales" ,r-scales))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/ggcyto/issues") (synopsis "Visualize Cytometry data with ggplot") (description "With the dedicated fortify method implemented for @code{flowSet}, @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper and some custom layers also make it easy to add gates and population statistics to the plot.") (license license:artistic2.0))) (define-public r-flowviz (package (name "r-flowviz") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-flowcore" ,r-flowcore) ("r-hexbin" ,r-hexbin) ("r-idpmisc" ,r-idpmisc) ("r-kernsmooth" ,r-kernsmooth) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-mass" ,r-mass) ("r-rcolorbrewer" ,r-rcolorbrewer))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) (define-public r-flowclust (package (name "r-flowclust") (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments `(#:configure-flags (list "--configure-args=--enable-bundled-gsl=no"))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-corpcor" ,r-corpcor) ("r-ellipse" ,r-ellipse) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) (inputs `(("gsl" ,gsl))) (native-inputs `(("pkg-config" ,pkg-config) ("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowClust") (synopsis "Clustering for flow cytometry") (description "This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.") (license license:artistic2.0))) ;; TODO: this package bundles an old version of protobuf. It's not easy to ;; make it use our protobuf package instead. (define-public r-rprotobuflib (package (name "r-rprotobuflib") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'unpack-bundled-sources (lambda _ (with-directory-excursion "src" (invoke "tar" "xf" "protobuf-3.10.0.tar.gz")) #t))))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/RProtoBufLib/") (synopsis "C++ headers and static libraries of Protocol buffers") (description "This package provides the headers and static library of Protocol buffers for other R packages to compile and link against.") (license license:bsd-3))) (define-public r-flowworkspace (package (name "r-flowworkspace") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (propagated-inputs `(("r-aws-s3" ,r-aws-s3) ("r-aws-signature" ,r-aws-signature) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-digest" ,r-digest) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-ggplot2" ,r-ggplot2) ("r-graph" ,r-graph) ("r-lattice" ,r-lattice) ("r-latticeextra" ,r-latticeextra) ("r-matrixstats" ,r-matrixstats) ("r-ncdfflow" ,r-ncdfflow) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-scales" ,r-scales) ("r-xml" ,r-xml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/flowWorkspace/") (synopsis "Infrastructure for working with cytometry data") (description "This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.") (license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-cluster" ,r-cluster) ("r-fda" ,r-fda) ("r-flowcore" ,r-flowcore) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-kernsmooth" ,r-kernsmooth) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rrcov" ,r-rrcov))) (home-page "http://www.github.com/RGLab/flowStats") (synopsis "Statistical methods for the analysis of flow cytometry data") (description "This package provides methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the @code{flowCore} package.") (license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-clue" ,r-clue) ("r-data-table" ,r-data-table) ("r-flowclust" ,r-flowclust) ("r-flowcore" ,r-flowcore) ("r-flowstats" ,r-flowstats) ("r-flowviz" ,r-flowviz) ("r-flowworkspace" ,r-flowworkspace) ("r-graph" ,r-graph) ("r-gtools" ,r-gtools) ("r-ks" ,r-ks) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-ncdfflow" ,r-ncdfflow) ("r-plyr" ,r-plyr) ("r-r-utils" ,r-r-utils) ("r-rbgl" ,r-rbgl) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) ("r-rrcov" ,r-rrcov))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-linking (lambda _ (substitute* "src/Makevars.in" ;; This is to avoid having a plain directory on the list of ;; libraries to link. (("\\{h5lib\\}" match) (string-append match "/libhdf5.a"))) #t))))) (inputs `(("libxml2" ,libxml2))) (propagated-inputs `(("r-base64enc" ,r-base64enc) ("r-bh" ,r-bh) ("r-biobase" ,r-biobase) ("r-corpcor" ,r-corpcor) ("r-cytolib" ,r-cytolib) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-ggcyto" ,r-ggcyto) ("r-graph" ,r-graph) ("r-jsonlite" ,r-jsonlite) ("r-lattice" ,r-lattice) ("r-opencyto" ,r-opencyto) ("r-plyr" ,r-plyr) ("r-rbgl" ,r-rbgl) ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo) ("r-rcppparallel" ,r-rcppparallel) ("r-rgraphviz" ,r-rgraphviz) ("r-rhdf5lib" ,r-rhdf5lib) ("r-rprotobuflib" ,r-rprotobuflib) ("r-runit" ,r-runit) ("r-tibble" ,r-tibble) ("r-xml" ,r-xml) ("r-xml2" ,r-xml2) ("r-yaml" ,r-yaml))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://github.com/RGLab/CytoML") (synopsis "GatingML interface for cross platform cytometry data sharing") (description "This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.") (license license:artistic2.0))) (define-public r-flowsom (package (name "r-flowsom") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-consensusclusterplus" ,r-consensusclusterplus) ("r-cytoml" ,r-cytoml) ("r-flowcore" ,r-flowcore) ("r-flowworkspace" ,r-flowworkspace) ("r-igraph" ,r-igraph) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-tsne" ,r-tsne) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/FlowSOM/") (synopsis "Visualize and interpret cytometry data") (description "FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.") (license license:gpl2+))) (define-public r-mixomics (package (name "r-mixomics") (version "6.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs `(("r-corpcor" ,r-corpcor) ("r-dplyr" ,r-dplyr) ("r-ellipse" ,r-ellipse) ("r-ggrepel" ,r-ggrepel) ("r-ggplot2" ,r-ggplot2) ("r-gridextra" ,r-gridextra) ("r-igraph" ,r-igraph) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-rarpack" ,r-rarpack) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-reshape2" ,r-reshape2) ("r-tidyr" ,r-tidyr))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://www.mixOmics.org") (synopsis "Multivariate methods for exploration of biological datasets") (description "mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs `(("r-beanplot" ,r-beanplot) ("r-dosnow" ,r-dosnow) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-foreach" ,r-foreach) ("r-ggplot2" ,r-ggplot2) ("r-gmodels" ,r-gmodels) ("r-gplots" ,r-gplots) ("r-mass" ,r-mass) ("r-matrixstats" ,r-matrixstats) ("r-mixomics" ,r-mixomics) ("r-moments" ,r-moments) ("r-rcpp" ,r-rcpp) ("r-rcppeigen" ,r-rcppeigen) ("r-reshape2" ,r-reshape2) ("r-robustbase" ,r-robustbase) ("r-viridis" ,r-viridis))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/DepecheR/") (synopsis "Identify traits of clusters in high-dimensional entities") (description "The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs `(("r-aucell" ,r-aucell) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-feather" ,r-feather) ("r-gseabase" ,r-gseabase) ("r-r-utils" ,r-r-utils) ("r-summarizedexperiment" ,r-summarizedexperiment))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the @dfn{transcription start site} (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-cicero (package (name "r-cicero") (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-fnn" ,r-fnn) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-glasso" ,r-glasso) ("r-gviz" ,r-gviz) ("r-igraph" ,r-igraph) ("r-iranges" ,r-iranges) ("r-matrix" ,r-matrix) ("r-monocle" ,r-monocle) ("r-plyr" ,r-plyr) ("r-reshape2" ,r-reshape2) ("r-s4vectors" ,r-s4vectors) ("r-stringi" ,r-stringi) ("r-stringr" ,r-stringr) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) ("r-vgam" ,r-vgam))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description "Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs `(("r-monocle3" ,r-monocle3) ,@(alist-delete "r-monocle" (package-propagated-inputs r-cicero))))))) (define-public r-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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. (snippet '(begin (for-each delete-file-recursively '("src/LZ4" "src/XZ" "src/ZLIB")) (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") (("(ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") "CoreArray/dVLIntGDS.o") (("PKG_LIBS = ./liblzma.a") "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) (string-append "include <" header ">"))) #t)))) (properties `((upstream-name . "gdsfmt"))) (build-system r-build-system) (inputs `(("lz4" ,lz4) ("xz" ,xz) ("zlib" ,zlib))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "http://corearray.sourceforge.net/") (synopsis "R Interface to CoreArray Genomic Data Structure (GDS) Files") (description "This package provides a high-level R interface to CoreArray @dfn{Genomic Data Structure} (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The @code{gdsfmt} package offers efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package @code{parallel}.") (license license:lgpl3))) (define-public r-bigmelon (package (name "r-bigmelon") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-gdsfmt" ,r-gdsfmt) ("r-geoquery" ,r-geoquery) ("r-methylumi" ,r-methylumi) ("r-minfi" ,r-minfi) ("r-watermelon" ,r-watermelon))) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) (define-public r-seqbias (package (name "r-seqbias") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-genomicranges" ,r-genomicranges) ("r-rhtslib" ,r-rhtslib))) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") (version "0.99.20") (source (origin (method url-fetch) (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" version 'annotation)) (sha256 (base32 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) (build-system r-build-system) ;; As this package provides little more than a very large data file it ;; doesn't make sense to build substitutes. (arguments `(#:substitutable? #f)) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-bsgenome" ,r-bsgenome) ("r-biostrings" ,r-biostrings))) (home-page "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") (description "This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).") (license license:artistic2.0))) (define-public r-reqon (package (name "r-reqon") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs `(("r-rjava" ,r-rjava) ("r-rsamtools" ,r-rsamtools) ("r-seqbias" ,r-seqbias))) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description "This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.") (license license:gpl2))) (define-public r-wavcluster (package (name "r-wavcluster") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi")))) (properties `((upstream-name . 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The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package integrates RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn")))) (properties `((upstream-name . 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(license license: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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"GenomeGraphs"))) (build-system r-build-system) (propagated-inputs `(("r-biomart" ,r-biomart))) (home-page "https://bioconductor.org/packages/GenomeGraphs/") (synopsis "Plotting genomic information from Ensembl") (description "Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.") (license license:artistic2.0))) (define-public r-wavetiling (package (name "r-wavetiling") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "waveTiling" version)) (sha256 (base32 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) (properties `((upstream-name . "waveTiling"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-biostrings" ,r-biostrings) ("r-genomegraphs" ,r-genomegraphs) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-oligo" ,r-oligo) ("r-oligoclasses" ,r-oligoclasses) ("r-preprocesscore" ,r-preprocesscore) ("r-waveslim" ,r-waveslim))) (home-page "https://r-forge.r-project.org/projects/wavetiling/") (synopsis "Wavelet-based models for tiling array transcriptome analysis") (description "This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.") (license license:gpl2+))) (define-public r-variancepartition (package (name "r-variancepartition") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah")))) (properties `((upstream-name . 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The package includes dream differential expression analysis for repeated measures.") (license license:gpl2+))) (define-public r-htqpcr (package (name "r-htqpcr") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-gplots" ,r-gplots) ("r-limma" ,r-limma) ("r-rcolorbrewer" ,r-rcolorbrewer))) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).") (license license:artistic2.0))) (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv")))) (properties `((upstream-name . 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"ActiveDriverWGS"))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) ("r-bsgenome" ,r-bsgenome) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) ("r-s4vectors" ,r-s4vectors))) (native-inputs `(("r-knitr" ,r-knitr))) (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") (synopsis "Driver discovery tool for cancer whole genomes") (description "This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.") (license license:gpl3))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. 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