;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2023 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2022 Efraim Flashner ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022, 2023 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet ;;; Copyright © 2023 Navid Afkhami ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . 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The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.") (license license:gpl2+))) (define-public r-absseq (package (name "r-absseq") (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 "1my2slp88qpb15qidjd646hlslvn8brv6i553h21c4c76jzxzsiz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) (home-page "https://bioconductor.org/packages/ABSSeq") (synopsis "RNA-Seq analysis based on modelling absolute expression differences") (description "This package implements a new RNA-Seq analysis method and integrates two modules: a basic model for pairwise comparison and a linear model for complex design. RNA-Seq quantifies gene expression with reads count, which usually consists of conditions (or treatments) and several replicates for each condition. This software infers differential expression directly by the counts difference between conditions. It assumes that the sum counts difference between conditions follow a negative binomial distribution. In addition, @code{ABSSeq} moderates the fold-changes by two steps: the expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.") (license license:gpl3+))) (define-public r-adacgh2 (package (name "r-adacgh2") (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 (base32 "1mmckrxhv23kl3g4d3n4hfdm97sfg2k36khzy9i6d73g7c033hsv")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-adam (package (name "r-adam") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 "1hy7xdf6v2fqggvc9rdl90gn0l6vfbmvb23c61i8q45s3qsaxksp")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-dt r-go-db r-keggrest r-knitr r-pbapply r-rcpp r-stringr r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ADAM") (synopsis "Gene activity and diversity analysis module") (description "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA) package created to group a set of genes from comparative samples (control versus experiment) belonging to different species according to their respective functions. The corresponding roles are extracted from the default collections like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG). @code{ADAM} show their significance by calculating the p-values referring to gene diversity and activity. Each group of genes is called @dfn{Group of functionally associated genes} (GFAG).") (license license:gpl2+))) (define-public r-adamgui (package (name "r-adamgui") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 "0jc0sbmmc98z75x73ns3qwcvklvx73wqla87cki8sls6ywa8w93j")))) (properties `((upstream-name . 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Features such as differential expression and fold change can be easily seen with aid of the plots made with the @code{GFAGpathUi} function.") (license license:gpl2+))) (define-public r-adimpute (package (name "r-adimpute") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 "0a3r4bkf6g28lgsq21077ag9ba6zrfv6yflawx9fg73zdx4266jp")))) (properties `((upstream-name . 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The @code{ADImpute} package proposes two methods to address this issue: @enumerate @item a gene regulatory network-based approach using gene-gene relationships learnt from external data; @item a baseline approach corresponding to a sample-wide average. @end enumerate @code{ADImpute} implements these novel methods and also combines them with existing imputation methods like @code{DrImpute} and @code{SAVER}. @code{ADImpute} can learn the best performing method per gene and combine the results from different methods into an ensemble.") (license license:gpl3+))) (define-public r-adsplit (package (name "r-adsplit") (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 "0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 "0g7n6dj1scad833y2182946hn3yh4jad20wvw9ic8gmqb438vihj")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs (list r-matrix r-rlang r-s4vectors r-singlecellexperiment r-summarizedexperiment r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/jasonratcliff/aggregateBioVar") (synopsis "Differential gene expression analysis for multi-subject scRNA-seq") (description "This package @code{aggregateBioVar} contains tools to summarize single cell gene expression profiles at the level of subject for single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates). A @code{SingleCellExperiment} object is taken as input and converted to a list of @code{SummarizedExperiment} objects, where each list element corresponds to an assigned cell type. The @code{SummarizedExperiment} objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.") (license license:gpl3))) (define-public r-agilp (package (name "r-agilp") (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 "0rm646iqc8hf8vfk0pdg064hm9k4k371bp1q4k7z2l16zhs8a07r")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-agimicrorna (package (name "r-agimicrorna") (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 "1gydc2sy0lf2h83dzr60w9k3ipqd8h62q6764xpn31girwx70rdz")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs (list r-affy r-affycoretools r-biobase r-limma r-preprocesscore)) (home-page "https://git.bioconductor.org/packages/AgiMicroRna") (synopsis "Processing and differential expression analysis of Agilent microRNA chips") (description "@code{AgiMicroRna} provides useful functionality for the processing, quality assessment and differential expression analysis of Agilent microRNA array data. The package uses a limma-like structure to generate the processed data in order to make statistical inferences about differential expression using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.") (license license:gpl3))) (define-public r-aims (package (name "r-aims") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 "1mbwv70ypkb3x086css94m89wq9pqzd23i7nar1844vbqpw3j83q")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) (home-page "https://git.bioconductor.org/packages/AIMS") (synopsis "Absolute assignment of breast cancer intrinsic molecular subtype") (description "This package contains an implementation of @code{AIMS} -- Absolute Intrinsic Molecular Subtyping. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.") (license license:artistic2.0))) (define-public r-airpart (package (name "r-airpart") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 "024vcxf23irlysc8srqii3zqhhldpwdcj0i4zzhz18x3bdy9cbj0")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs (list r-apeglm r-clue r-complexheatmap r-dplyr r-dynamictreecut r-emdbook r-forestplot r-ggplot2 r-lpsolve r-matrixstats r-mclust r-pbapply r-plyr r-rcolorbrewer r-rlang r-s4vectors r-scater r-singlecellexperiment r-smurf r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/airpart") (synopsis "Differential cell-type-specific allelic imbalance") (description "The airpart package identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. 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Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.") (license license:gpl2))) (define-public r-decipher (package (name "r-decipher") (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 "16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n")))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-dbi r-iranges r-rsqlite r-s4vectors r-xvector)) (home-page "https://www.bioconductor.org/packages/DECIPHER/") (synopsis "Tools for deciphering and managing biological sequences") (description "This package provides a toolset for deciphering and managing biological sequences.") (license license:gpl3))) (define-public r-deco (package (name "r-deco") (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deco" version)) (sha256 (base32 "0d4abif3v62cbas6hl7pfw8q8jihh7nsra76k9cm6kz54qw4fbnw")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-dss (package (name "r-dss") (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 "1aslbzwqfp609ym98k6cjjf6r1ns9hxcpx4igfjhqf2v0pazz2q8")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DSS") (synopsis "Dispersion shrinkage for sequencing data") (description "DSS is an R library performing differential analysis for count-based sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from @dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-dyndoc (package (name "r-dyndoc") (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 "16cb4pby6ja0xy8ygbgr6zfbyp4agyhlds5sayc5ryq50vafykah")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") (synopsis "Dynamic document tools") (description "This package provides a set of functions to create and interact with dynamic documents and vignettes.") 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A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells.") (license license:bsd-3))) (define-public r-iranges (package (name "r-iranges") (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 "013a3vcw1v5vn0sg2d9cwrdksch48kilvxp8cr79y0nr4vk58q9z")))) (properties `((upstream-name . 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(define-public r-absfiltergsea (package (name "r-absfiltergsea") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "AbsFilterGSEA" version)) (sha256 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description "This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.") (license license:gpl2))) ;; This is a CRAN package, but it depends on r-biobase from Bioconductor. 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(license license:gpl3))) ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs (package (name "r-deconstructsigs") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "deconstructSigs" version)) (sha256 (base32 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) (properties `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb r-reshape2)) (home-page "https://github.com/raerose01/deconstructSigs") (synopsis "Identifies signatures present in a tumor sample") (description "This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.") 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(license license:gpl3))) (define-public r-limma (package (name "r-limma") (version "3.56.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 "0miyba9frn1p4pkclzpr0bfazsk0br2jgpwpwwh773d3103hkn0r")))) (build-system r-build-system) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") (description "This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.") (license license:gpl2+))) (define-public r-maaslin2 (package (name "r-maaslin2") (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Maaslin2" version)) (sha256 (base32 "06mb72hbzihdficv73yqbb2m86bkw78w3vbw1rm98n0npxq2fch6")))) (properties `((upstream-name . "Maaslin2"))) (build-system r-build-system) (propagated-inputs (list r-biglm r-car r-chemometrics r-cplm r-data-table r-dplyr r-edger r-ggplot2 r-glmmtmb r-hash r-lme4 r-lmertest r-logging r-mass r-metagenomeseq r-optparse r-pbapply r-pcapp r-pheatmap r-pscl r-robustbase r-tibble r-vegan)) (native-inputs (list r-knitr)) (home-page "http://huttenhower.sph.harvard.edu/maaslin2") (synopsis "Multivariable association discovery in population-scale meta-omics studies") (description "MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. This package relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.") (license license:expat))) (define-public r-made4 (package (name "r-made4") (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 "1233l5160msxp85vm2h0j3k073vv5d9wj55709x4s657fi9la6ij")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-gplots r-rcolorbrewer r-scatterplot3d r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "http://www.hsph.harvard.edu/aedin-culhane/") (synopsis "Multivariate analysis of microarray data using ADE4") (description "This is a package for multivariate data analysis and graphical display of microarray data. Functions are included for supervised dimension reduction (between group analysis) and joint dimension reduction of two datasets (coinertia analysis).") (license license:artistic2.0))) (define-public r-makecdfenv (package (name "r-makecdfenv") (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "makecdfenv" version)) (sha256 (base32 "1a6kngwmc7nvzlgpnhdv4j180847gjh4i3dshld0pcvy3b6bjv8r")))) (properties `((upstream-name . "makecdfenv"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list r-affy r-affyio r-biobase r-zlibbioc)) (home-page "https://bioconductor.org/packages/makecdfenv") (synopsis "Chip description file environment maker") (description "This package implements two functions. One of them reads an Affymetrix @acronym{CDF, chip description file} and creates a hash table environment containing the location/probe set membership mapping. The other one creates a package that automatically loads that environment.") (license license:gpl2+))) (define-public r-manor (package (name "r-manor") (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MANOR" version)) (sha256 (base32 "0ili9xy7vvw17mz44lxadv1vkf3ahpks2l34qa9yfccpalwhzriw")))) (properties `((upstream-name . "MANOR"))) (build-system r-build-system) (propagated-inputs (list r-glad)) (native-inputs (list r-knitr)) (home-page "http://bioinfo.curie.fr/projects/manor/index.html") (synopsis "CGH micro-array normalization") (description "This package ofers functions for importation, normalization, visualization, and quality control to correct identified sources of variability in array of @acronym{CGH, comparative genomic hybridization} experiments.") (license license:gpl2))) (define-public r-maser (package (name "r-maser") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maser" version)) (sha256 (base32 "1ma5d1i56gw8hm2pgvzzvmdd1cm2xb42rgf5lb6sf4v47yzlyb9f")))) (properties `((upstream-name . "maser"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-data-table r-dplyr r-dt r-genomeinfodb r-genomicranges r-ggplot2 r-gviz r-iranges r-reshape2 r-rtracklayer)) (native-inputs (list r-knitr)) (home-page "https://github.com/DiogoVeiga/maser") (synopsis "Mapping alternative splicing events to proteins") (description "This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.") (license license:expat))) (define-public r-metagenomeseq (package (name "r-metagenomeseq") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metagenomeSeq" version)) (sha256 (base32 "0293c531l0sjz8qxy7nrajfl081v9df0af9242017msbvyszq6wk")))) (properties `((upstream-name . "metagenomeSeq"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-foreach r-glmnet r-gplots r-limma r-matrix r-matrixstats r-rcolorbrewer r-wrench)) (native-inputs (list r-knitr)) (home-page "https://github.com/HCBravoLab/metagenomeSeq") (synopsis "Statistical analysis for sparse high-throughput sequencing") (description "MetagenomeSeq is designed to determine features (be it @acronym{OTU, Operational Taxanomic Unit}, species, etc.) that are differentially abundant between two or more groups of multiple samples. This package is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.") (license license:artistic2.0))) (define-public r-metaneighbor (package (name "r-metaneighbor") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 "151ip70la12kj80c0airi1yyjbj69gnkshd6kfk88wsvq7s179id")))) (properties `((upstream-name . "MetaNeighbor"))) (build-system r-build-system) (propagated-inputs (list r-beanplot r-dplyr r-ggplot2 r-gplots r-igraph r-matrix r-matrixstats r-rcolorbrewer r-singlecellexperiment r-summarizedexperiment r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MetaNeighbor") (synopsis "Single cell replicability analysis") (description "This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. @code{MetaNeighbor} works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.") (license license:expat))) (define-public r-methylkit (package (name "r-methylkit") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 "1qi4gwlxsxr4cgs8s12qybrs89vr79xwd7n9in1af3hyn0swikn1")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-emdbook r-fastseg r-genomeinfodb r-genomicranges r-gtools r-iranges r-kernsmooth r-limma r-mclust r-mgcv r-qvalue r-r-utils r-rcpp r-rhtslib r-rsamtools r-rtracklayer r-s4vectors r-zlibbioc)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://github.com/al2na/methylKit") (synopsis "DNA methylation analysis from high-throughput bisulfite sequencing results") (description "MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from @dfn{Reduced representation bisulfite sequencing} (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) (define-public r-mfuzz (package (name "r-mfuzz") (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Mfuzz" version)) (sha256 (base32 "0rfna5ycwkx4xb2gv1wpfn7f7nz6f79w5nlkb7719l5730d81wnz")))) (properties `((upstream-name . "Mfuzz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) (home-page "http://mfuzz.sysbiolab.eu/") (synopsis "Soft clustering of time series gene expression data") (description "This is a package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).") (license license:gpl2))) (define-public r-mmuphin (package (name "r-mmuphin") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 (base32 "14cn1mg9ffhzy1vgschl2h0wzah3c1g67q367f2m050a3z2i2ndy")) ;; Delete generated files. (snippet '(for-each delete-file '("inst/doc/MMUPHin.R" "inst/doc/MMUPHin.html"))))) (properties `((upstream-name . "MMUPHin"))) (build-system r-build-system) (arguments (list #:phases #~(modify-phases %standard-phases (add-after 'unpack 'fix-includes (lambda _ (substitute* "inst/doc/MMUPHin.Rmd" (("\\.\\./man/figures") (string-append (getcwd) "/man/figures")) (("bibliography: references.bib") (string-append "bibliography: " (getcwd) "/vignettes/references.bib"))))) ;; Maaslin2 generates log files with timestamps. We don't need to ;; keep them. The generated PDF files also contain timestamps, so ;; we replace them with arbitrary fixed timestamps. (add-after 'check 'make-reproducible (lambda _ (for-each delete-file (find-files #$output "maaslin2.log")) (with-fluids ((%default-port-encoding "ISO-8859-1")) (substitute* (find-files #$output "\\.pdf$") (("/CreationDate \\(D:.*\\)") "/CreationDate (D:20230301143558)") (("/ModDate \\(D:.*\\)") "/ModDate (D:20230301143558)")))))))) ;; The DESCRIPTION file says that glpk is needed, but this package does ;; not seem to reference the library directly. (propagated-inputs (list r-cowplot r-dplyr r-fpc r-ggplot2 r-igraph r-maaslin2 r-metafor r-stringr r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MMUPHin") (synopsis "Meta-analysis with uniform pipeline for heterogeneity in microbiome") (description "MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: @itemize @item covariate-controlled batch- and cohort effect adjustment; @item meta-analysis differential abundance testing; @item meta-analysis unsupervised discrete structure (clustering) discovery; @item meta-analysis unsupervised continuous structure discovery. @end itemize") (license license:expat))) (define-public r-motifrg (package (name "r-motifrg") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-iranges r-seqlogo r-xvector)) (home-page "https://bioconductor.org/packages/motifRG") (synopsis "Discover motifs in high throughput sequencing data") (description "This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods.") (license license:artistic2.0))) (define-public r-muscat (package (name "r-muscat") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 "1jcy07m8ywpgsmwkq6s7zj32w7gvxqj52j562irv2h2q429awdxk")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-blme r-complexheatmap r-data-table r-deseq2 r-dplyr r-edger r-ggplot2 r-glmmtmb r-limma r-lme4 r-lmertest r-matrix r-matrixstats r-progress r-purrr r-s4vectors r-scales r-scater r-sctransform r-scuttle r-singlecellexperiment r-summarizedexperiment r-variancepartition r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/HelenaLC/muscat") (synopsis "Multi-sample multi-group scRNA-seq data analysis tools") (description "This package @code{muscat} provides various methods and visualization tools for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.") (license license:gpl3))) (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 "1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome ;; These two packages are suggested packages r-bsgenome-hsapiens-1000genomes-hs37d5 r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-dplyr r-genomeinfodb r-genomicranges r-ggalluvial r-ggdendro r-ggplot2 r-iranges r-magrittr r-nmf r-pracma r-purrr r-rcolorbrewer r-s4vectors r-stringr r-tibble r-tidyr r-variantannotation)) (home-page "https://bioconductor.org/packages/MutationalPatterns/") (synopsis "Extract and visualize mutational patterns in genomic data") (description "This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.") (license license:expat))) (define-public r-msa (package (name "r-msa") (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 "08fg4y8rmkvilsx2hxqwxa90p2wqrl4iyndp7wfjicvplmaxp708")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-iranges r-rcpp r-s4vectors)) (native-inputs (list r-knitr)) (home-page "http://www.bioinf.jku.at/software/msa/") (synopsis "Multiple sequence alignment") (description "The msa package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.") (license license:gpl2+))) (define-public r-msnbase (package (name "r-msnbase") (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 "0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-biocgenerics r-biocparallel r-digest r-ggplot2 r-impute r-iranges r-lattice r-maldiquant r-mass r-mscoreutils r-mzid r-mzr r-pcamethods r-plyr r-protgenerics r-rcpp r-s4vectors r-scales r-vsn r-xml)) (native-inputs (list r-knitr)) (home-page "https://github.com/lgatto/MSnbase") (synopsis "Base functions and classes for MS-based proteomics") (description "This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.") (license license:artistic2.0))) (define-public r-msnid (package (name "r-msnid") (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 "1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-annotationdbi r-annotationhub r-biobase r-biocgenerics r-biocstyle r-biostrings r-data-table r-doparallel r-dplyr r-foreach r-ggplot2 r-iterators r-msnbase r-msmstests r-mzid r-mzr r-protgenerics r-purrr r-r-cache r-rcpp r-reshape2 r-rlang r-runit r-stringr r-tibble r-xtable)) (home-page "https://bioconductor.org/packages/MSnID") (synopsis "Utilities for LC-MSn proteomics identifications") (description "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) (define-public r-mzid (package (name "r-mzid") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 "0grl7798vnpxb6nw98zj0lbvsrhkjfsyn0y15bi4v7vhyhkk26xm")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-iterators r-plyr r-protgenerics r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/mzID") (synopsis "Parser for mzIdentML files") (description "This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.") (license license:gpl2+))) (define-public r-mzr (package (name "r-mzr") (version "2.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 "1jsna4xwyph1gg72wwqlpavb65g5nc3db1vmcs1qcw1mdgasdjhk")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "mzR") (updater-extra-inputs . ("boost")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-boost (lambda _ (substitute* "src/Makevars" (("\\./boost/libs.*") "") (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ") (("\\ARCH_OBJS=" line) (string-append line "\nBOOST_LIBS=-lboost_system -lboost_regex \ -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))))))) (inputs (list boost ; use this instead of the bundled boost sources zlib)) (propagated-inputs (list r-biobase r-biocgenerics r-ncdf4 r-protgenerics r-rcpp r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") (description "The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-numbat (package (name "r-numbat") (version "1.3.2-1") (source (origin (method url-fetch) (uri (cran-uri "numbat" version)) (sha256 (base32 "1b9bykgw3z7a8bky5yv2g402gdapv8kcla2kbbyqvs77x4wba4q4")))) (properties `((upstream-name . "numbat"))) (build-system r-build-system) (propagated-inputs (list r-ape r-catools r-data-table r-dendextend r-dplyr r-genomicranges r-ggplot2 r-ggraph r-ggtree r-glue r-igraph r-iranges r-logger r-magrittr r-matrix r-optparse r-paralleldist r-patchwork r-pryr r-purrr r-r-utils r-rcpp r-rcpparmadillo r-rhpcblasctl r-roptim r-scales r-scistreer r-stringr r-tibble r-tidygraph r-tidyr r-vcfr r-zoo)) (home-page "https://github.com/kharchenkolab/numbat") (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") (description "This package provides a computational method that infers copy number variations (CNV) in cancer scRNA-seq data and reconstructs the tumor phylogeny. It integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. It does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). It can be used to: @enumerate @item detect allele-specific copy number variations from single-cells @item differentiate tumor versus normal cells in the tumor microenvironment @item infer the clonal architecture and evolutionary history of profiled tumors @end enumerate For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, Gao et al in Nature Biotechnology 2022}.") (license license:expat))) (define-public r-organism-dplyr (package (name "r-organism-dplyr") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 "0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationfilter r-biocfilecache r-dbi r-dbplyr r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-rlang r-rsqlite r-s4vectors r-tibble)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Organism.dplyr") (synopsis "Dplyr-based access to Bioconductor annotation resources") (description "This package provides an alternative interface to Bioconductor @code{ annotation} resources, in particular the gene identifier mapping functionality of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate functionality of the @code{TxDb} packages (e.g., @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).") 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(license license:artistic2.0))) (define-public r-oscope (package (name "r-oscope") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 "055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) (home-page "https://bioconductor.org/packages/Oscope") (synopsis "Oscillatory genes identifier in unsynchronized single cell RNA-seq") (description "Oscope is a oscillatory genes identifier in unsynchronized single cell RNA-seq. This statistical pipeline has been developed to identify and recover the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.") (license license:asl2.0))) (define-public r-pcaexplorer (package (name "r-pcaexplorer") (version "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 "04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-pcamethods (package (name "r-pcamethods") (version "1.92.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 "14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-mass r-rcpp)) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") (description "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.") (license license:gpl3+))) (define-public r-pfamanalyzer (package (name "r-pfamanalyzer") (version "1.0.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pfamAnalyzeR" version)) (sha256 (base32 "0zff887lc4bjrv683kqsw47vjwmf6886wybklsf2wd6hpy23mxfy")))) (properties `((upstream-name . "pfamAnalyzeR"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-magrittr r-readr r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/pfamAnalyzeR") (synopsis "Identification of domain isotypes in pfam data") (description "This R package enables the user to read pfam predictions into R. Most human protein domains exist as multiple distinct variants termed domain isotypes. This R package enables the identification and classification of such domain isotypes from pfam data.") (license license:expat))) ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs (package (name "r-pscbs") (version "0.66.0") (source (origin (method url-fetch) (uri (cran-uri "PSCBS" version)) (sha256 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) (properties `((upstream-name . "PSCBS"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. 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"ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") (synopsis "S4 generic functions for proteomics infrastructure") (description "This package provides S4 generic functions needed by Bioconductor proteomics packages.") (license license:artistic2.0))) (define-public r-rbgl (package (name "r-rbgl") (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 "0y6ghiwraw3whs57i31qnvlvqlbl9143wxv2yg48rp7qxipxvn6s")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs (list r-bh r-graph)) (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description "This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.") (license license:artistic2.0))) (define-public r-rcas (package (name "r-rcas") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 "073fhbh0pzyca90q2irbaiwj21sci8jf9ksflx9pm9fr1giy37i4")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-cowplot r-data-table r-dt r-genomation r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-ggseqlogo r-gprofiler2 r-iranges r-knitr r-pbapply r-pheatmap r-plotly r-plotrix r-proxy r-ranger r-rsqlite r-rtracklayer r-rmarkdown r-s4vectors pandoc)) (native-inputs (list r-knitr)) (synopsis "RNA-centric annotation system") (description "RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.") 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(license license:bsd-2))) (define-public r-rsamtools (package (name "r-rsamtools") (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 "18kh6vmyjmv7zklqr5ifpfixjwldxgwj550c69mqfkk7m0zk52cl")))) (properties `((upstream-name . 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(define-public r-restfulr (package (name "r-restfulr") (version "0.0.15") (source (origin (method url-fetch) (uri (cran-uri "restfulr" version)) (sha256 (base32 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0")))) (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description "This package models a RESTful service as if it were a nested R list.") (license license:artistic2.0))) (define-public r-rtcga (package (name "r-rtcga") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGA" version)) (sha256 (base32 "1y7ciq1270dc1c9y490fygrsylyzwl52fqi1vj7r75hy3rnwnv25")))) (properties `((upstream-name . 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Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.") (license license:gpl2))) (define-public r-rtcgatoolbox (package (name "r-rtcgatoolbox") (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RTCGAToolbox" version)) (sha256 (base32 "03p5rgjzc1265q60jkvk92vhcib5wdnv6bz997r70q9c39y03wm5")))) (properties `((upstream-name . "RTCGAToolbox"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-data-table r-delayedarray r-genomeinfodb r-genomicranges r-httr r-raggedexperiment r-rcircos r-rcurl r-rjsonio r-rvest r-s4vectors r-stringr r-summarizedexperiment r-tcgautils)) (native-inputs (list r-knitr)) (home-page "http://mksamur.github.io/RTCGAToolbox/") (synopsis "Export TCGA Firehose data") (description "Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. This package provides an extensible R based data client for Firehose pre-processed data.") (license license:gpl2))) (define-public r-rtracklayer (package (name "r-rtracklayer") (version "1.60.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 "06z02sz8zjg2lxp2q4qwhvh6dsi6srirdmhcdvmi3as50nnjmzd8")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-zlib (lambda _ (substitute* "DESCRIPTION" ((" zlibbioc,") "")) (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs (list pkg-config)) (inputs (list openssl zlib)) (propagated-inputs (list r-biocgenerics r-biocio r-biostrings r-genomeinfodb r-genomicalignments r-genomicranges r-iranges r-rcurl r-restfulr r-rsamtools r-s4vectors r-xml r-xvector r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description "rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-samr (package (name "r-samr") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "samr" version)) (sha256 (base32 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-scannotatr (package (name "r-scannotatr") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 (base32 "0mxq2dknrhgj1487kfshkayx963c7qdgxwmlh9fbfr0lwc7gljfn")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-ape r-caret r-data-tree r-dplyr r-e1071 r-ggplot2 r-kernlab r-proc r-rocr r-seurat r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/grisslab/scAnnotatR") (synopsis "Pretrained models for prediction on single cell RNA-sequencing data") (description "This package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables to quickly get a first annotation of the cell types present in the dataset without requiring prior knowledge. The package also lets you train using own models to predict new cell types based on specific research needs.") (license license:expat))) (define-public r-scdblfinder (package (name "r-scdblfinder") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 (base32 "0lvacrgfj9i8mwlcv5ykxs69hd3bm6bvr6fsddxffsr7cckpn31w")))) (properties `((upstream-name . 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The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.") 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An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) (define-public r-lefser (package (name "r-lefser") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 "1ifmbbsbyzcyvjni9ww27c9qsqliv7vj2rv9mg9c7gnqgbg6h2c4")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-lumi (package (name "r-lumi") (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 "1lxxqr7x9jdjrsj5j95jb0dbd7p208vifxw3j4s4140zh1ppxnpj")))) (build-system r-build-system) (propagated-inputs (list r-affy r-annotate r-annotationdbi r-biobase r-dbi r-genomicfeatures r-genomicranges r-kernsmooth r-lattice r-mass r-methylumi r-mgcv r-nleqslv r-preprocesscore r-rsqlite)) (home-page "https://bioconductor.org/packages/lumi") (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") (description "The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.") (license license:lgpl2.0+))) (define-public r-linnorm (package (name "r-linnorm") (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 "1sqkmjah2lxahnvwv04a970za2b8kzvmxnb41k9xrnvj0akigc2d")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs (list r-amap r-apcluster r-ellipse r-fastcluster r-fpc r-ggdendro r-ggplot2 r-gmodels r-igraph r-limma r-mass r-mclust r-rcpp r-rcpparmadillo r-rtsne r-statmod r-vegan r-zoo)) (native-inputs (list r-knitr)) (home-page "http://www.jjwanglab.org/Linnorm/") (synopsis "Linear model and normality based transformation method") (description "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function (@code{Linnorm}), the following pipelines are implemented: @enumerate @item Library size/batch effect normalization (@code{Linnorm.Norm}) @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or hierarchical clustering (@code{Linnorm.tSNE}, @code{Linnorm.PCA}, @code{Linnorm.HClust}) @item Differential expression analysis or differential peak detection using limma (@code{Linnorm.limma}) @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) @item Stable gene selection for scRNA-seq data; for users without or who do not want to rely on spike-in genes (@code{Linnorm.SGenes}) @item Data imputation (@code{Linnorm.DataImput}). @end enumerate Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the @code{RnaXSim} function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.") (license license:expat))) (define-public r-ioniser (package (name "r-ioniser") (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-biostrings r-bit64 r-dplyr r-ggplot2 r-magrittr r-rhdf5 r-shortread r-stringr r-tibble r-tidyr r-xvector)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/IONiseR/") (synopsis "Quality assessment tools for Oxford Nanopore MinION data") (description "IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.") (license license:expat))) ;; This is a CRAN package, but it depends on multtest from Bioconductor. (define-public r-mutoss (package (name "r-mutoss") (version "0.1-13") (source (origin (method url-fetch) (uri (cran-uri "mutoss" version)) (sha256 (base32 "0hgi9wpy3ai23dk6cdba6r118vvmgw210racsg3n1p24rv6ny3xn")))) (properties `((upstream-name . "mutoss"))) (build-system r-build-system) (propagated-inputs (list r-multcomp r-multtest r-mvtnorm 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 "1.8") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mathjaxr r-mutoss r-qqconf r-rdpack 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-tradeseq (package (name "r-tradeseq") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 "14b90x9h34mhbc4sdpzkygrrswf84pi1ddwpzxhvlvr9gs443xqs")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-edger r-ggplot2 r-igraph r-magrittr r-mass r-matrix r-matrixstats r-mgcv r-pbapply r-princurve r-rcolorbrewer r-s4vectors r-singlecellexperiment r-slingshot r-summarizedexperiment r-tibble r-trajectoryutils r-viridis)) (native-inputs (list r-knitr)) (home-page "https://statomics.github.io/tradeSeq/index.html") (synopsis "Trajectory-based differential expression analysis") (description "This package provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.") (license license:expat))) (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 (list r-biocgenerics r-iranges 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 "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 "1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel r-biostrings r-bsgenome r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-matrix r-rsamtools r-rtracklayer r-s4vectors r-variantannotation)) (home-page "https://bioconductor.org/packages/VariantTools/") (synopsis "Tools for exploratory analysis of variant calls") (description "Explore, diagnose, and compare variant calls using filters. The VariantTools package supports a workflow for loading data, calling single sample variants and tumor-specific somatic mutations or other sample-specific variant types (e.g., RNA editing). Most of the functions operate on alignments (BAM files) or datasets of called variants. 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 "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 "031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs (list 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 "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 "15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-rcpp)) (native-inputs (list 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 "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 "0ic12p1qyfrmh3l1wv7s9yi8sr84crj4nksmcx0lybb6rak9gy0x")))) (build-system r-build-system) (propagated-inputs (list r-multtest 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 "1.66.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sigPathway" version)) (sha256 (base32 "0k86hlz7zbbw7559bd2sl59pr441kihgwvg8nr75mj8d50n783sy")))) (properties `((upstream-name . "sigPathway"))) (build-system r-build-system) (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") (synopsis "Pathway analysis") (description "This package is used to conduct pathway analysis by calculating the NT_k and NE_k statistics in a statistical framework for determining whether a specified group of genes for a pathway has a coordinated association with a phenotype of interest.") (license license:gpl2))) (define-public r-fcscan (package (name "r-fcscan") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 (base32 "071sylwwj27bk39pkn5a29r7bmfpmyaixkkg7dqcdq230c1dsrps")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs (list r-doparallel r-foreach r-genomicranges r-iranges r-plyr r-rtracklayer r-summarizedexperiment r-variantannotation)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/fcScan") (synopsis "Detect clusters of coordinates with user defined options") (description "This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a \"greedy\" option allowing thus the presence of additional sites within the allowed window size.") (license license:artistic2.0))) (define-public r-fgsea (package (name "r-fgsea") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 "0chnrwiwk31crrx4am1yrbxjdqd3jycgjgczqzj7lxaa9v7lvm7z")))) (build-system r-build-system) (propagated-inputs (list r-bh r-biocparallel r-cowplot r-data-table r-fastmatch r-ggplot2 r-matrix r-rcpp r-scales)) (native-inputs (list 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 "3.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 "1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocparallel r-fgsea r-ggplot2 r-gosemsim r-hdo-db r-qvalue r-reshape2)) (native-inputs (list 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-enrichedheatmap (package (name "r-enrichedheatmap") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EnrichedHeatmap" version)) (sha256 (base32 "18p2vjcg76rrjzjl03zgm4yxrgllbd42hg8rvsdbfb0s7brzr7ya")))) (properties `((upstream-name . "EnrichedHeatmap"))) (build-system r-build-system) (propagated-inputs (list r-circlize r-complexheatmap r-genomicranges r-getoptlong r-iranges r-locfit r-matrixstats r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/EnrichedHeatmap") (synopsis "Enriched heatmaps") (description "Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. This type of heatmap is just a normal heatmap but with some special settings, with the functionality of @code{ComplexHeatmap}, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.") (license license:expat))) (define-public r-enrichplot (package (name "r-enrichplot") (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 "0yxnh5bmfcfsciwm852rbb707v9zbky3lsz2xsyyaapm5jjb6npk")))) (build-system r-build-system) (propagated-inputs (list r-aplot r-dose r-ggnewscale r-ggplot2 r-ggraph r-ggtree r-gosemsim r-igraph r-magrittr r-plyr r-purrr r-rcolorbrewer r-reshape2 r-rlang r-scatterpie r-shadowtext r-yulab-utils)) (native-inputs (list 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. All the visualization methods are developed based on ggplot2 graphics.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we ;; added it here. (define-public r-classdiscovery (package (name "r-classdiscovery") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "ClassDiscovery" version)) (sha256 (base32 "06l7jvpcdynij05hb0ka33zpg7xdyqyzfzx24s0bnlspp83yc62s")))) (properties `((upstream-name . "ClassDiscovery"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-mclust r-oompabase r-oompadata)) (native-inputs (list r-xtable)) ;for vignettes (home-page "https://oompa.r-forge.r-project.org/") (synopsis "Classes and methods for \"Class Discovery\" with Microarrays or Proteomics") (description "This package defines classes for \"class discovery\" in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.") (license license:asl2.0))) (define-public r-clusterprofiler (package (name "r-clusterprofiler") (version "4.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 "1kihrpa8cb2bqk5dck0w6yzgfpl72qxlrxwpidg1ar27q3ivz8w3")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-dose r-downloader r-dplyr r-enrichplot r-go-db r-gosemsim r-gson r-magrittr r-plyr r-qvalue r-rlang r-tidyr r-yulab-utils)) (native-inputs (list r-knitr)) (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") (synopsis "Analysis and visualization of functional profiles for gene clusters") (description "This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.") (license license:artistic2.0))) (define-public r-clusterexperiment (package (name "r-clusterexperiment") (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 "0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-ape r-biocgenerics r-biocsingular r-cluster r-delayedarray r-edger r-hdf5array r-howmany r-kernlab r-limma r-locfdr r-matrix r-matrixstats r-mbkmeans r-nmf r-phylobase r-pracma r-rcolorbrewer r-rcpp r-s4vectors r-scales r-singlecellexperiment r-stringr r-summarizedexperiment r-zinbwave)) (home-page "https://bioconductor.org/packages/clusterExperiment/") (synopsis "Compare clusterings for single-cell sequencing") (description "This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.") 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A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "1qyvwhmdv27xsyljyzyh52pn6x0wqx8rslvr2j7vqcjyywv270x6")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-ggplot2 r-ggrepel r-iranges r-limma r-qqman r-s4vectors r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiDataSet/") (synopsis "Implementation of MultiDataSet and ResultSet") (description "This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. 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While performing similarly to PLS, OPLS facilitates interpretation. This package provides imlementations of PCA, PLS, and OPLS for multivariate analysis and feature selection of omics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients).") 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(license license:artistic2.0))) (define-public r-opencyto (package (name "r-opencyto") (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "0z0p09mkap1jqlq1x33i2ik87pbhwq85xgqyfsx4r360nhv06pna")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-data-table r-flowclust r-flowcore r-flowviz r-flowworkspace r-graph r-ncdfflow r-rbgl r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") 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The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p")))) (properties `((upstream-name . 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This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-chicago (package (name "r-chicago") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s")))) (properties `((upstream-name . 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(define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 "0gagfm7v5bnnfj1zy6zf4cg91bj8nvv4vm38f3a1s4q2xc8pcvfj")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-cistopic (package (name "r-cistopic") (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs (list r-aucell r-data-table r-dplyr r-dosnow r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description "The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as @dfn{Latent Dirichlet Allocation} (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.") (license license:gpl3))) (define-public r-cistopic-next (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803") (revision "1")) (package (inherit r-cistopic) (name "r-cistopic-next") ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd ;; since the previous release is 2.1.0. Oh well. (version (git-version "0.3.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . 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It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.") (license license:expat))) (define-public r-biscuiteer (package (name "r-biscuiteer") (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 "07nak6mfw9m8ldl336sqgkl3638ibv1hxwd89hwxdrn914wz3hw3")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-tricycle (package (name "r-tricycle") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 "1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-circular r-dplyr r-genomicranges r-ggnewscale r-ggplot2 r-iranges r-rcolorbrewer r-s4vectors r-scater r-scattermore r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hansenlab/tricycle") (synopsis "Transferable representation and inference of cell cycle") (description "The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The @code{tricycle} provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.") (license license:gpl3))) (define-public r-tximeta (package (name "r-tximeta") (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 "02240v41scaqxabjb62zh6shkkzb9520dhn0lfc2jbimnb26yj7f")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-phyloseq (package (name "r-phyloseq") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 (base32 "0rmv8f1m8ck97v991wdly3fma2rjczhi974lh7ikwx6rcx6fp9ah")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-ape r-biobase r-biocgenerics r-biomformat r-biostrings r-cluster r-data-table r-foreach r-ggplot2 r-igraph r-multtest r-plyr r-reshape2 r-scales r-vegan)) (native-inputs (list r-knitr)) (home-page "https://github.com/joey711/phyloseq") (synopsis "Handling and analysis of high-throughput microbiome census data") (description "Phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.") (license license:agpl3))) ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;