;;; 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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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 . "ADaCGH2"))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'python3-compatibility (lambda _ (substitute* "inst/imagemap-example/toMap.py" (("print nameMap") "print(nameMap)"))))))) (inputs (list python-wrapper)) (propagated-inputs (list r-acgh r-bit r-cluster r-dnacopy r-ff r-glad r-snapcgh r-tilingarray r-waveslim)) (home-page "https://github.com/rdiaz02/adacgh2") (synopsis "Big data analysis from aCGH experiments") (description "This package analyzes and creates plots of array @acronym{CGH, comparative genomic hybridization} data. Also, it allows usage of @acronym{CBS, Circular Binary Segementation}, wavelet-based smoothing, HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use @code{ff} for storing data.") (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.") 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Specifically, the package includes @dfn{Analysis of Compositions of Microbiomes with Bias Correction}(ANCOM-BC) and @dfn{Analysis of Composition of Microbiomes} (ANCOM) for DA analysis, and @dfn{Sparse Estimation of Correlations among Microbiomes} (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the @code{ANCOMBC} package were designed to correct these biases and construct statistically consistent estimators.") (license license:artistic2.0))) (define-public r-animalcules (package (name "r-animalcules") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 "1z46lpd2zi3b88i27qm48wy4acb2xsjh63zgxhfx2y4bgvr29ni7")))) (properties `((upstream-name . 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It provides as output the @code{stanfit} object as well as posterior median and credible interval estimates for each correlation element.") (license license:expat))) (define-public r-barcodetrackr (package (name "r-barcodetrackr") (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 "155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs (list r-circlize r-cowplot r-dplyr r-ggdendro r-ggplot2 r-ggridges r-magrittr r-plyr r-proxy r-rcolorbrewer r-rlang r-s4vectors r-scales r-shiny r-summarizedexperiment r-tibble r-tidyr r-vegan r-viridis)) (native-inputs (list r-knitr)) (home-page "https://github.com/dunbarlabNIH/barcodetrackR") (synopsis "Functions for analyzing cellular barcoding data") (description "This package is developed for the analysis and visualization of clonal tracking data. 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(license license:gpl2))) (define-public r-debcam (package (name "r-debcam") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh")) (snippet '(for-each delete-file '("inst/java/CornerDetect.jar" "inst/java/lib/pj20150107.jar"))))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-drimseq (package (name "r-drimseq") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 (base32 "1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-edger r-genomicranges r-ggplot2 r-iranges r-limma r-mass r-reshape2 r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DRIMSeq") (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq") (description "The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. 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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-bluster (package (name "r-bluster") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 "15f103lpl686730vl8g69fhki9iq2ncgr5dm6qm2xc9bq9vh65s9")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs (list r-biocneighbors r-biocparallel r-cluster r-igraph r-matrix r-rcpp r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/bluster") (synopsis "Clustering algorithms for Bioconductor") (description"This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. 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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-isva (package (name "r-isva") (version "1.9") (source (origin (method url-fetch) (uri (cran-uri "isva" version)) (sha256 (base32 "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z")))) (properties `((upstream-name . "isva"))) (build-system r-build-system) (propagated-inputs (list r-fastica r-jade r-qvalue)) (home-page "https://cran.r-project.org/package=isva") (synopsis "Independent surrogate variable analysis") (description "Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors (see Teschendorff AE et al 2011, ).") (license license:gpl2))) (define-public r-italics (package (name "r-italics") (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 (base32 "09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08")))) (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. (define-public r-bisquerna (package (name "r-bisquerna") (version "1.0.5") (source (origin (method url-fetch) (uri (cran-uri "BisqueRNA" version)) (sha256 (base32 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n")))) (properties `((upstream-name . "BisqueRNA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-limsolve)) (native-inputs (list r-knitr)) (home-page "https://www.biorxiv.org/content/10.1101/669911v1") (synopsis "Decomposition of bulk expression with single-cell sequencing") (description "This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.") (license license:gpl3))) ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs (package (name "r-deconstructsigs") (version "1.8.0") (source (origin (method url-fetch) (uri (cran-uri "deconstructSigs" version)) (sha256 (base32 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) (properties `((upstream-name . "deconstructSigs"))) (build-system r-build-system) (propagated-inputs (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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"Harshlight"))) (build-system r-build-system) (propagated-inputs (list r-affy r-altcdfenvs r-biobase)) (home-page "http://asterion.rockefeller.edu/Harshlight/") (synopsis "Corrective make-up program for microarray chips") (description "The package detects extended diffuse and compact blemishes on microarray chips. Harshlight marks the areas in a collection of chips (affybatch objects). A corrected @code{AffyBatch} object will result. The package replaces the defected areas with @code{N/A}s or the median of the values of the same probe. The new version handles the substitute value as a whole matrix to solve the memory problem.") (license license:gpl2+))) (define-public r-hpar (package (name "r-hpar") (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 "1sg0mjada72a13xh3k6xsiaff7xj4mp76r6i8iab8nfkvng07p4i")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp"))) (add-after 'unpack 'avoid-internet-access (lambda _ (setenv "GUIX_BUILD" "yes") (substitute* "R/zzz.R" (("ExperimentHub::createHubAccessors.*" m) (string-append "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) (propagated-inputs (list r-experimenthub)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") (description "This package provides a simple interface to and data from the Human Protein Atlas project.") 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"lfa"))) (build-system r-build-system) (propagated-inputs (list r-corpcor)) (native-inputs (list r-knitr)) (home-page "https://github.com/StoreyLab/lfa") (synopsis "Logistic Factor Analysis for categorical data") (description "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.") (license license:gpl3))) (define-public r-limma (package (name "r-limma") (version "3.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 "02c559an6hzk00bbvlrq1qljsnby4a53ng9jj6ff570mc6pabjn6")))) (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. 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(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 . 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"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-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 . 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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 . 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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 . 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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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The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) (define-public r-rhdf5 (package (name "r-rhdf5") (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 "1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description "This R/Bioconductor package provides an interface between HDF5 and R. 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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.") 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The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-samr (package (name "r-samr") (version "3.0") (source (origin (method url-fetch) (uri (cran-uri "samr" version)) (sha256 (base32 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15")))) (properties `((upstream-name . 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However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. @code{scmap} is a method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.") (license license:gpl3))) (define-public r-scry (package (name "r-scry") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 "0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz")))) (properties `((upstream-name . 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It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) ;; This is a CRAN package but it depends on a bioconductor package. (define-public r-speaq (package (name "r-speaq") (version "2.7.0") (source (origin (method url-fetch) (uri (cran-uri "speaq" version)) (sha256 (base32 "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) (properties `((upstream-name . "speaq"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-data-table r-dosnow r-foreach r-ggplot2 r-gridextra r-impute r-massspecwavelet r-missforest r-reshape2 r-rfast r-rvest r-xml2)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=speaq") (synopsis "Tools for nuclear magnetic resonance spectra alignment") (description "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance} spectroscopy data analysis as easy as possible. 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Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) (define-public r-topgo (package (name "r-topgo") (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 "0avjjvih387qhw8n4vjz4jq66q7sicgacsw53b85lq2c6ppib662")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-variantannotation (package (name "r-variantannotation") (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 "0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biostrings r-bsgenome r-dbi r-genomeinfodb r-genomicfeatures r-genomicranges r-iranges r-matrixgenerics r-summarizedexperiment r-rhtslib r-rsamtools r-rtracklayer r-s4vectors r-xvector r-zlibbioc)) (build-system r-build-system) (home-page "https://bioconductor.org/packages/VariantAnnotation") (synopsis "Package for annotation of genetic variants") (description "This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.") (license license:artistic2.0))) (define-public r-vsn (package (name "r-vsn") (version "3.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 "0i6c0wyhj0gcq0mw13zyk60cza2baq4yrj1n2dzqgsqkmhm5lfla")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") (description "The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to \"normalized log-ratios\". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) ;; There is no source tarball, so we fetch the code from the Bioconductor git ;; repository. (define-public r-xcir (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277") (revision "1")) (package (name "r-xcir") (version (git-version "1.8.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://git.bioconductor.org/packages/XCIR") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p")))) (properties `((upstream-name . "XCIR"))) (build-system r-build-system) (propagated-inputs (list r-biomart r-biostrings r-data-table r-ggplot2 r-iranges r-readxl r-s4vectors r-seqminer r-variantannotation)) (native-inputs (list r-knitr)) (home-page "https://github.com/SRenan/XCIR") (synopsis "Analysis of X chromosome inactivation") (description "This package is an R package that offers models and tools for subject level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape inference.") (license license:gpl2)))) (define-public r-xina (package (name "r-xina") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 (base32 "1byk8xgn9rwfbi677b99ysxi4a9n58fr3hbnwjzhnziy2n2cd703")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs (list r-alluvial r-ggplot2 r-gridextra r-igraph r-mclust r-plyr r-stringdb)) (native-inputs (list r-knitr)) (home-page "https://git.bioconductor.org/packages/XINA") (synopsis "Identifying proteins that exhibit similar patterns") (description "The aim of @code{XINA} is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. @code{XINA} imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. @code{XINA} not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.") (license license:gpl3))) (define-public r-xmapbridge (package (name "r-xmapbridge") (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 (base32 "09pskmhjymqvhk26mk5yy1k195v536a2qp4k6xdd67xhf5ag260i")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") (synopsis "Display numeric data in the web based genome browser X:MAP") (description "The package @code{xmapbridge} can plot graphs in the X:Map genome browser. X:Map uses the Google Maps API to provide a scrollable view of the genome. It supports a number of species, and can be accessed at @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a suitable format. Graph plotting in R is done using calls to the functions @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be similar to those used by the standard plot methods in R. These result in data being written to a set of files (in a specific directory structure) that contain the data to be displayed, as well as some additional meta-data describing each of the graphs.") (license license:lgpl3))) (define-public r-xvector (package (name "r-xvector") (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 "1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2")))) (properties `((upstream-name . 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(license license:gpl2))) (define-public r-qvalue (package (name "r-qvalue") (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 "1552390pf3wrrir6c9xshgll69a33fhbdnh2cvpnznma1ag490ki")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) (native-inputs (list 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 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 "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs (list r-emdbook r-genomicranges r-rcpp r-rcppeigen r-rcppnumerical r-summarizedexperiment)) (native-inputs (list r-knitr r-rmarkdown)) (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 "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 "1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs (list r-bsgenome r-genomeinfodb r-genomicalignments r-genomicranges r-mass r-rsamtools r-rtracklayer 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 "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 "1p5fxfpvjz85a2n1jsmj3niqzymnlsja9b53q2yxvj327qq58z8a")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs (list r-amap r-apeglm r-ashr r-biocparallel r-deseq2 r-dplyr r-genomicalignments r-genomicranges r-ggplot2 r-ggrepel r-gplots r-greylistchip r-iranges r-lattice r-limma r-locfit r-rcolorbrewer r-rcpp r-rhtslib r-rsamtools r-s4vectors r-summarizedexperiment r-systempiper)) (home-page "https://bioconductor.org/packages/DiffBind") (synopsis "Differential binding analysis of ChIP-Seq peak data") (description "This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.") (license license:artistic2.0))) (define-public r-ripseeker (package (name "r-ripseeker") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs (list r-s4vectors r-iranges r-genomicranges r-summarizedexperiment r-rsamtools r-genomicalignments 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-mbecs (package (name "r-mbecs") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MBECS" version)) (sha256 (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz")))) (properties `((upstream-name . 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In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.") (license license:artistic2.0))) (define-public r-mbkmeans (package (name "r-mbkmeans") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 "0c48ycgba1m10p1w2qz9r7yxw15nqzlz8fp44d6lbrvj3svmgjwi")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-beachmat r-benchmarkme r-biocparallel r-clusterr r-delayedarray r-matrix r-rcpp r-rcpparmadillo r-rhdf5lib r-s4vectors r-singlecellexperiment r-summarizedexperiment)) (home-page "https://bioconductor.org/packages/mbkmeans") (synopsis "Mini-batch k-means clustering for single-cell RNA-seq") (description "This package implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.") (license license:expat))) (define-public r-multibac (package (name "r-multibac") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiBaC" version)) (sha256 (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i")))) (properties `((upstream-name . "MultiBaC"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-matrix r-multiassayexperiment r-pcamethods r-plotrix r-ropls)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MultiBaC") (synopsis "Multiomic batch effect correction") (description "MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.") (license license:gpl3))) (define-public r-multtest (package (name "r-multtest") (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 "19c6l8pkyp0m2zdzhr81cnmx5lqf501sap9h6ig5iiv66sf2ysmz")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase 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 "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 "184izzxc8bpagcac8wqinjp8kmf9zpvjibl0g32nnr64kp9f4rsn")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description "This package implements some simple graph handling capabilities for R.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-ggm (package (name "r-ggm") (version "2.5") (source (origin (method url-fetch) (uri (cran-uri "ggm" version)) (sha256 (base32 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) (properties `((upstream-name . 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It mimics many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates.") (license license:artistic2.0))) (define-public r-lpsymphony (package (name "r-lpsymphony") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 "096d0dql1cg85mmxba3dy2a7ba3sxqphsviqqvx1n35xiidsnpyp")))) (build-system r-build-system) (arguments (list #:phases '(modify-phases %standard-phases (add-after 'unpack 'make-build-order-reproducible (lambda _ (substitute* '("src/SYMPHONY/Cgl/configure.ac" "src/SYMPHONY/Cgl/configure") (("for file in `ls \\*/Makefile.in`") "for file in `ls */Makefile.in | sort`"))))))) (inputs (list zlib)) (native-inputs (list pkg-config r-knitr)) (home-page "https://r-forge.r-project.org/projects/rsymphony") (synopsis "Symphony integer linear programming solver in R") (description "This package was derived from Rsymphony. 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It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) (define-public r-leidenbase (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96") (revision "1")) (package (name "r-leidenbase") (version (git-version "0.1.9" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/leidenbase") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f")))) (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. 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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 "2.24.0") (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.") 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GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests: @enumerate @item the Wilcoxon rank-sum test that is used when genes are ranked, @item a binomial test that is used when genes are associated with two counts, and @item a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts. @end enumerate To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.") (license license:gpl2+))) (define-public r-abaenrichment (package (name "r-abaenrichment") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABAEnrichment" version)) (sha256 (base32 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044")))) (properties `((upstream-name . "ABAEnrichment"))) (build-system r-build-system) (propagated-inputs (list r-abadata r-data-table r-gofuncr r-gplots r-gtools r-rcpp)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ABAEnrichment/") (synopsis "Gene expression enrichment in human brain regions") (description "The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function @code{aba_enrich} integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.") (license license:gpl2+))) (define-public r-annotationfuncs (package (name "r-annotationfuncs") (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFuncs" version)) (sha256 (base32 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr")))) (properties `((upstream-name . "AnnotationFuncs"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi 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 "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 "0dwbh2h2mp8gy0kwqmkri3q2glnzcj8cn83j1qyh7lk15anc33g8")))) (properties `((upstream-name . 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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 "4.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 "0z0ajmy1zx7mqcjm2ibyk2qg3cj00kl76padyksbdbmwdncxs8yb")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs (list r-abind r-biocgenerics r-fftwtools r-htmltools r-htmlwidgets r-jpeg r-locfit r-png r-rcurl r-tiff)) (native-inputs (list 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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 "0kjlp62s2393jdwp0crizsgp4iqagbgnd3hdl9vpbr9qrjxg4s7m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-data-table r-ebimage r-iranges r-limma r-matrix r-mzr r-s4vectors r-summarizedexperiment)) (native-inputs (list 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 "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 "1kk7ysscq8xdbn35b20s8sn8gl93sy0c718fmvr1yrhiqaxq5alr")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) (native-inputs (list 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 "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 "075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biostrings r-genomeinfodb r-genomicranges r-ggbio r-ggplot2 r-iranges r-nmf r-pcamethods r-proxy r-reshape2 r-s4vectors r-variantannotation)) (native-inputs (list 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 "1.25.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 "0xva7vljq2k78rzjnjlp4x3ylwk86jaqn2cgbff4h4sb8rfdya7c")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-bsgenome-hsapiens-ucsc-hg19 r-circlize r-complexheatmap r-corrplot r-dendextend r-doparallel r-dplyr r-genomeinfodb r-genomicranges r-getoptlong r-ggbeeswarm r-ggplot2 r-gridextra r-gtrellis r-keggrest r-limsolve r-magrittr r-pmcmrplus r-pracma r-reshape2 r-somaticsignatures r-variantannotation)) (native-inputs (list 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 "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 "0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p")))) (build-system r-build-system) (propagated-inputs (list r-affy r-affyio r-biobase r-biocmanager r-biostrings 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 (list r-affy r-biobase r-biocgenerics r-gcrma 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 (list 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 "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 "08m94q65c11isbkx9xljm2bx2aq2rml1bqh5i1cg81xg2ilm9h6a")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-doparallel r-foreach r-ggplot2 r-iterators r-minfi r-rcolorbrewer)) (native-inputs (list 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 "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 "0ddfl4jp0n8sb665hcpsij959fl28rj22n1h61wp2374kpc0fwfj")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biomart r-downloader r-edger r-gplots r-limma r-matrixstats r-preprocesscore r-quantro r-rcolorbrewer r-readr)) (native-inputs (list 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 "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 "0p5q6nyp8d0gl95rd89xrs08gv87m1q6d0x4ws2b6sd4gc1nw2ny")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-genomeinfodb r-genomicalignments r-genomicranges r-iranges r-rtracklayer r-s4vectors r-summarizedexperiment)) (home-page "https://github.com/vodkatad/roar/") (synopsis "Identify differential APA usage from RNA-seq alignments") (description "This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.") (license license:gpl3))) (define-public r-xbseq (package (name "r-xbseq") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XBSeq" version)) (sha256 (base32 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz")))) (properties `((upstream-name . "XBSeq"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-deseq2 r-dplyr r-ggplot2 r-locfit r-magrittr r-matrixstats r-pracma r-roar)) (native-inputs (list r-knitr)) (home-page "https://github.com/Liuy12/XBSeq") (synopsis "Test for differential expression for RNA-seq data") (description "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential expression} (DE), where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. 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(arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'set-HOME (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-dplyr r-igraph r-logger r-magrittr r-matrix r-omnipathr r-progress r-purrr r-rcurl r-rlang r-tibble r-tidyr)) (native-inputs (list r-knitr)) (home-page "https://github.com/AnaGalhoz37/wppi") (synopsis "Weighting protein-protein interactions") (description "This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.") (license license:expat))) (define-public r-wrench (package (name "r-wrench") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 "18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h")))) (properties `((upstream-name . 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(license license:asl2.0))) (define-public r-widgettools (package (name "r-widgettools") (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 "03bvh2jk97jj40z35q5n1is2wxrs4dggw08ndyywy4pzx1diqdc4")))) (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. 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The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.") (license license:artistic2.0))) (define-public r-zfpkm (package (name "r-zfpkm") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 "1fkzyq282xafyapgi5xi1c2dmfkyikqvf622pycjs80fas38044h")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr)) (native-inputs (list 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).") 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(license license:artistic2.0))) (define-public r-rhisat2 (package (name "r-rhisat2") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 "1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy")))) (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 (list r-genomicfeatures r-genomicranges r-sgseq)) (native-inputs (list 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 "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "09k4r5a735022rc33k6a7pr98qxwy8ijsn451hcw18dimqzm78bx")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biocparallel r-biostrings r-bsgenome r-genomeinfodb r-genomicfeatures r-genomicfiles r-genomicranges r-iranges r-rbowtie r-rhtslib r-rsamtools r-rtracklayer r-s4vectors r-shortread)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/QuasR/") (synopsis "Quantify and annotate short reads in R") (description "This package provides a framework for the quantification and analysis of short genomic reads. 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It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.") (license license:gpl2+))) (define-public r-birewire (package (name "r-birewire") (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "1741raw1834093y5zhgx9jywfgz0wl0idlkynvab2c8vi40kc9a8")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs (list r-igraph r-matrix r-rtsne r-slam)) (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") (synopsis "Tools for randomization of bipartite graphs") (description "This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. 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.") 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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. 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 "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "1cq5ixaxag5r6nvl73c8bznxkdjhxw1r7qx90ml7qm4jr7wyi173")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-ggplot2 r-multiassayexperiment r-multidataset r-plotly r-summarizedexperiment)) (native-inputs (list 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).") 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The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "1vjbk1vpqjxy9wv2a6sc32yyk0bhkbvdx9hl3vs5yjifwdswh2pw")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-annotationhub r-dplyr r-genomeinfodb r-genomicfeatures r-genomicranges r-ggplot2 r-iranges r-readr r-regioner r-reshape2 r-rtracklayer r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/annotatr/") (synopsis "Annotation of genomic regions to genomic annotations") (description "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. 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 "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs (list 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. 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"flowWorkspace"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-cytolib r-data-table r-delayedarray r-dplyr r-flowcore r-ggplot2 r-graph r-matrixstats r-ncdfflow r-rbgl r-rgraphviz r-rhdf5lib r-rprotobuflib r-s4vectors r-scales r-xml)) (native-inputs (list 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 "4.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "13mdpdndalm0d6azjancw0xcbdc674ivkj8kp6ccfpdd7gydhr4j")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-cluster r-corpcor r-fda r-flowcore r-flowviz r-flowworkspace r-kernsmooth r-ks r-lattice r-mass r-mnormt r-ncdfflow r-rcolorbrewer 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 "2.12.0") (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.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs (list libxml2 #;zlib )) (propagated-inputs (list r-bh r-biobase r-cpp11 r-cytolib r-data-table r-dplyr r-flowcore r-flowworkspace r-ggcyto r-graph r-jsonlite r-opencyto r-rbgl r-rgraphviz r-rhdf5lib r-rprotobuflib r-tibble r-xml r-yaml)) (native-inputs (list 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 "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "13y0ny61skj14mfhjwpa5zmflzdqxy2vf6gd4m9358g4wxfbhkv0")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-colorramps r-consensusclusterplus r-dplyr r-flowcore r-ggforce r-ggnewscale r-ggplot2 r-ggpubr r-igraph r-magrittr r-rlang r-rtsne r-tidyr 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 "6.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0dqndpmi56g772sra49vdrkjs4m9h2gzimwv3bwmw2l0krh2ax8s")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-corpcor r-dplyr r-ellipse r-ggrepel r-ggplot2 r-gridextra r-igraph r-lattice r-mass r-matrixstats r-rarpack r-rcolorbrewer r-reshape2 r-tidyr)) (native-inputs (list 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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "0dp2y85mfn995rvg698xnxlkz1kd8g0byjypxx62cpfldnkrinxl")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs (list r-arrow r-aucell r-biocgenerics r-data-table r-dplyr r-genomeinfodb r-genomicranges r-gseabase r-r-utils r-s4vectors r-summarizedexperiment r-tibble)) (native-inputs (list r-knitr)) (home-page "https://aertslab.org/#scenic") (synopsis "Identify transcription factor binding motifs enriched on a gene list") (description "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the @dfn{transcription start site} (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-chicago (package (name "r-chicago") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Chicago") (synopsis "Capture Hi-C analysis of genomic organization") (description "This package provides a pipeline for analysing Capture Hi-C data.") (license license:artistic2.0))) ;; This is a CRAN package, but it depends on Bioconductor packages, so we put ;; it here. (define-public r-ciara (package (name "r-ciara") (version "0.1.0") (source (origin (method url-fetch) (uri (cran-uri "CIARA" version)) (sha256 (base32 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-cicero (package (name "r-cicero") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "12zdygnwqjla99wzvvxzcmiwmh4v0rmnx4yix02gbj8xl4bxmm51")))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-biobase r-biocgenerics r-data-table r-dplyr r-fnn r-genomicranges r-ggplot2 r-glasso r-gviz r-igraph r-iranges r-matrix r-monocle r-plyr r-reshape2 r-s4vectors r-stringi r-stringr r-tibble r-tidyr r-vgam)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/cicero/") (synopsis "Predict cis-co-accessibility from single-cell data") (description "Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.") (license license:expat))) ;; This is the latest commit on the "monocle3" branch. (define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") (version "1.14.0") (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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(license license:gpl2+))) (define-public r-roc (package (name "r-roc") (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "0fq59bwc5i8zdw0v0jr5j5lm4hk6p7b88i2xndsgj4fq65yr50g1")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/ROC/") (synopsis "Utilities for ROC curves") (description "This package provides utilities for @dfn{Receiver Operating Characteristic} (ROC) curves, with a focus on micro arrays.") (license license:artistic2.0))) (define-public r-watermelon (package (name "r-watermelon") (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "0qslh2xhhyaf0nsgcqav6qgh05n8kp0s6p1zggc02iid30i1ibrj")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-illuminahumanmethylation450kanno-ilmn12-hg19 r-illuminaio r-limma r-lumi r-matrixstats r-methylumi r-roc)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/wateRmelon/") (synopsis "Illumina 450 methylation array normalization and metrics") (description "The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the @code{methylumi} and @code{minfi} packages.") (license license:gpl3))) (define-public r-gdsfmt (package (name "r-gdsfmt") (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "11qib2znznzvyb0x9qm1nfg9lhyqy63yrdjicy7n3n6l8dfd2lx7")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. (snippet '(begin (for-each delete-file-recursively '("src/LZ4" "src/XZ" "src/ZLIB")) (substitute* "src/Makevars" (("all: \\$\\(SHLIB\\)") "all:") (("\\$\\(SHLIB\\): liblzma.a") "") (("^ (ZLIB|LZ4)/.*") "") (("CoreArray/dVLIntGDS.cpp.*") "CoreArray/dVLIntGDS.cpp") (("CoreArray/dVLIntGDS.o.*") "CoreArray/dVLIntGDS.o") (("PKG_LIBS = ./liblzma.a") "PKG_LIBS = -llz4")) (substitute* "src/CoreArray/dStream.h" (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) (string-append "include <" header ">"))))))) (properties `((upstream-name . "gdsfmt") (updater-extra-inputs . 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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. 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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. ;;;