;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier ;;; Copyright © 2020 Peter Lo ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2021 Hong Li ;;; Copyright © 2021 Tim Howes ;;; Copyright © 2021 Nicolas Vallet ;;; ;;; This file is part of GNU Guix. ;;; ;;; GNU Guix is free software; you can redistribute it and/or modify it ;;; under the terms of the GNU General Public License as published by ;;; the Free Software Foundation; either version 3 of the License, or (at ;;; your option) any later version. ;;; ;;; GNU Guix is distributed in the hope that it will be useful, but ;;; WITHOUT ANY WARRANTY; without even the implied warranty of ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;;; GNU General Public License for more details. ;;; ;;; You should have received a copy of the GNU General Public License ;;; along with GNU Guix. If not, see . (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages docker) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages image) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) ;;; Annotations (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation)) (sha256 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs")))) (properties `((upstream-name . 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Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.") (license license:artistic2.0))) (define-public r-all (package (name "r-all") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z")))) (properties `((upstream-name . "ALL"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) (home-page "https://bioconductor.org/packages/ALL") (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") (description "The data consist of microarrays from 128 different individuals with @dfn{acute lymphoblastic leukemia} (ALL). 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This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.") (license license:gpl2+))) (define-public r-curatedtcgadata (package (name "r-curatedtcgadata") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) (sha256 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr")))) (properties `((upstream-name . 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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-adam (package (name "r-adam") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn")))) (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs (list r-adam r-colorramps r-data-table r-dplyr r-dt r-ggplot2 r-ggpubr r-ggrepel r-ggsignif r-go-db r-gridextra r-knitr r-rcolorbrewer r-reshape2 r-shiny r-shinyjs r-stringi r-stringr r-testthat r-varhandle)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ADAMgui/") (synopsis "GUI for gene activity and diversity analysis") (description "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI) for the @code{ADAM} package. The @code{ADAMgui} package provides two shiny-based applications that allows the user to study the output of the @code{ADAM} package files through different plots. It's possible, for example, to choose a specific @dfn{group of functionally associated genes} (GFAG) and observe the gene expression behavior with the plots created with the @code{GFAGtargetUi} function. 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 "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w")))) (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 "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1")))) (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 "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-agimicrorna (package (name "r-agimicrorna") (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa")))) (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-amountain (package (name "r-amountain") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/AMOUNTAIN") (synopsis "Modules for multilayer weighted gene co-expression networks") (description "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted gene co-expression network) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. @code{AMOUNTAIN} aims to search active modules in multi-layer WGCN using a continuous optimization approach.") (license license:gpl2+))) (define-public r-amaretto (package (name "r-amaretto") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) (properties `((upstream-name . 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This allows @code{AMARETTO} to identify novel cancer driver genes directing canonical cancer pathways.") (license license:asl2.0))) (define-public r-anaquin (package (name "r-anaquin") (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs (list r-deseq2 r-ggplot2 r-knitr r-locfit r-plyr r-qvalue r-rocr)) (native-inputs (list r-knitr)) (home-page "https://www.sequinstandards.com/") (synopsis "Statistical analysis of sequins") (description "The project is intended to support the use of @dfn{sequins}(synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.") 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(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.") 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In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These functions and data are also useful for gene set analysis using other methods.") (license license:gpl2+))) (define-public r-genefilter (package (name "r-genefilter") (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) (propagated-inputs (list r-annotate r-annotationdbi r-biobase r-biocgenerics r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description "This package provides basic functions for filtering genes from high-throughput sequencing experiments.") 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Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.") (license license:artistic2.0))) (define-public r-genomeinfodb (package (name "r-genomeinfodb") (version "1.32.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh")))) (properties `((upstream-name . 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The package is designed to deal with sequencing data from @dfn{Reduced representation bisulfite sequencing} (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) (define-public r-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 . 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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 "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961")))) (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 "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) (properties `((upstream-name . 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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))) (define-public r-organismdbi (package (name "r-organismdbi") (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) (properties `((upstream-name . 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(define-public r-pscbs (package (name "r-pscbs") (version "0.66.0") (source (origin (method url-fetch) (uri (cran-uri "PSCBS" version)) (sha256 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q")))) (properties `((upstream-name . "PSCBS"))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-before 'install 'change-home-dir (lambda _ ;; Change from /homeless-shelter to /tmp for write permission. (setenv "HOME" "/tmp")))))) (propagated-inputs (list r-aroma-light r-dnacopy r-future r-listenv r-matrixstats r-r-cache r-r-methodss3 r-r-oo r-r-utils)) (native-inputs (list r-r-rsp ;used to build vignettes r-r-devices)) (home-page "https://github.com/HenrikBengtsson/PSCBS") (synopsis "Analysis of parent-specific DNA copy numbers") (description "This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. 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(license license:artistic2.0))) (define-public r-reportingtools (package (name "r-reportingtools") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) (propagated-inputs (list r-annotate r-annotationdbi r-biobase r-biocgenerics r-category r-deseq2 r-edger r-ggbio r-ggplot2 r-gostats r-gseabase r-hwriter r-iranges r-knitr r-lattice r-limma r-pfam-db r-r-utils r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description "The ReportingTools package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser, or in other formats. 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(define-public r-restfulr (package (name "r-restfulr") (version "0.0.15") (source (origin (method url-fetch) (uri (cran-uri "restfulr" version)) (sha256 (base32 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0")))) (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjson r-s4vectors r-xml r-yaml)) (home-page "https://cran.r-project.org/package=restfulr") (synopsis "R interface to RESTful web services") (description "This package models a RESTful service as if it were a nested R list.") (license license:artistic2.0))) (define-public r-rtracklayer (package (name "r-rtracklayer") (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) (build-system r-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-zlib (lambda _ (substitute* "DESCRIPTION" ((" zlibbioc,") "")) (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") ""))))))) (native-inputs (list pkg-config)) (inputs (list zlib)) (propagated-inputs (list r-biocgenerics r-biocio r-biostrings r-genomeinfodb r-genomicalignments r-genomicranges r-iranges r-rcurl r-restfulr r-rsamtools r-s4vectors r-xml r-xvector r-zlibbioc)) (home-page "https://bioconductor.org/packages/rtracklayer") (synopsis "R interface to genome browsers and their annotation tracks") (description "rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). 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(license license:expat))) (define-public r-scdblfinder (package (name "r-scdblfinder") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-scmap (package (name "r-scmap") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-dplyr r-e1071 r-ggplot2 r-googlevis r-matrixstats r-proxy r-randomforest r-rcpp r-rcpparmadillo r-reshape2 r-s4vectors r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/hemberg-lab/scmap") (synopsis "Tool for unsupervised projection of single cell RNA-seq data") (description "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. 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-seqlogo (package (name "r-seqlogo") (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/seqLogo") (synopsis "Sequence logos for DNA sequence alignments") (description "seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") 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The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biocgenerics r-circlize r-clue r-cluster r-colorspace r-complexheatmap r-digest r-getoptlong r-globaloptions r-go-db r-gosemsim r-matrix r-org-hs-eg-db r-proxyc r-slam r-tm)) (native-inputs (list r-knitr)) (home-page "https://github.com/jokergoo/simplifyEnrichment") (synopsis "Simplify functional enrichment results") (description "This package provides a new clustering algorithm, binary cut, for clustering similarity matrices of functional terms is implemented in this package. 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This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events.") (license license:gpl3))) (define-public r-trajectoryutils (package (name "r-trajectoryutils") (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj")))) (properties `((upstream-name . 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The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.") (license license:gpl3))) (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39")))) (properties `((upstream-name . 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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 "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6")))) (properties `((upstream-name . 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(license license:lgpl2.1+))) (define-public r-tximport (package (name "r-tximport") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x")))) (build-system r-build-system) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") (description "This package provides tools to import transcript-level abundance, estimated counts and transcript lengths, and to summarize them into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on a Bioconductor package. (define-public r-valr (package (name "r-valr") (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k")))) (build-system r-build-system) (propagated-inputs (list r-broom r-dplyr r-ggplot2 r-rcpp r-readr r-rlang r-rtracklayer ;bioconductor package r-stringr r-tibble)) (native-inputs (list r-knitr)) (home-page "https://github.com/rnabioco/valr") (synopsis "Genome interval arithmetic in R") (description "This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.") 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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. 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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 "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10")))) (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. 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(define-public r-nbpseq (package (name "r-nbpseq") (version "0.3.1") (source (origin (method url-fetch) (uri (cran-uri "NBPSeq" version)) (sha256 (base32 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14")))) (properties `((upstream-name . "NBPSeq"))) (build-system r-build-system) (propagated-inputs (list r-qvalue)) (home-page "https://cran.r-project.org/web/packages/NBPSeq") (synopsis "Negative binomial models for RNA-Seq data") (description "This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.") (license license:gpl2))) (define-public r-ebseq (package (name "r-ebseq") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y")))) (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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) (build-system r-build-system) (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. The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code, while Rsymphony expects to find header and library files on the users' system. Thus the intention of @code{lpsymphony} is to provide an easy to install interface to SYMPHONY.") ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. ;; lpsimphony is released under the same terms. (license license:epl1.0))) (define-public r-ihw (package (name "r-ihw") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-fdrtool r-lpsymphony r-slam)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/IHW") (synopsis "Independent hypothesis weighting") (description "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.") (license license:artistic2.0))) (define-public r-icobra (package (name "r-icobra") (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9")))) (properties `((upstream-name . 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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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(let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f") (revision "1")) (package (name "r-sanssouci") (version (git-version "0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/pneuvial/sanssouci.git") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk")))) (build-system r-build-system) (propagated-inputs (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo)) (home-page "https://pneuvial.github.io/sanssouci") (synopsis "Post Hoc multiple testing inference") (description "The goal of sansSouci is to perform post hoc inference: in a multiple testing context, sansSouci provides statistical guarantees on possibly user-defined and/or data-driven sets of hypotheses.") 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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 "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf")))) (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. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.") (license license:gpl2))) (define-public r-rqc (package (name "r-rqc") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-biocstyle r-biostrings r-biovizbase r-genomicalignments r-genomicfiles r-ggplot2 r-iranges r-knitr r-markdown r-plyr r-rcpp r-reshape2 r-rsamtools r-s4vectors r-shiny r-shortread)) (native-inputs (list r-knitr)) (home-page "https://github.com/labbcb/Rqc") (synopsis "Quality control tool for high-throughput sequencing data") (description "Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. 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 "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm")))) (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.") (license license:gpl3))) (define-public r-birta (package (name "r-birta") (version "1.31.0") (source (origin (method url-fetch) (uri (bioconductor-uri "birta" version)) (sha256 (base32 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-limma r-mass)) (home-page "https://bioconductor.org/packages/birta") (synopsis "Bayesian inference of regulation of transcriptional activity") (description "Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of transcription factors and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.") (license license:gpl2+))) (define-public r-multidataset (package (name "r-multidataset") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf")))) (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 "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multiassayexperiment r-multidataset 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).") (license license:cecill))) (define-public r-biosigner (package (name "r-biosigner") (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-multiassayexperiment r-multidataset r-randomforest r-ropls r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") (synopsis "Signature discovery from omics data") (description "Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.") (license license:cecill))) (define-public r-annotatr (package (name "r-annotatr") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0")))) (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 "2.10.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl")))) (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. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.") (license license:gpl3))) (define-public r-flowutils (package (name "r-flowutils") (version "1.59.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowUtils" version)) (sha256 (base32 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26")))) (properties `((upstream-name . "flowUtils"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-corpcor r-flowcore r-graph r-runit r-xml)) (home-page "https://github.com/jspidlen/flowUtils") (synopsis "Utilities for flow cytometry") (description "This package provides utilities for flow cytometry data.") 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(define-public r-cycombine (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1")) (package (name "r-cycombine") (version (git-version "0.2.6" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/biosurf/cyCombine") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj")))) (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 "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-clue r-data-table r-flowclust r-flowcore r-flowstats r-flowviz r-flowworkspace r-graph r-gtools r-ks r-lattice r-mass r-ncdfflow r-plyr r-r-utils r-rbgl r-rcolorbrewer r-rcpp r-rrcov)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") 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The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.") (license license:gpl2+))) (define-public r-depecher (package ;Source/Weave error (name "r-depecher") (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im")))) (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 "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) (properties `((upstream-name . 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(define-public r-cicero-monocle3 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") (revision "1")) (package (inherit r-cicero) (name "r-cicero-monocle3") (version (git-version "1.3.2" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/cole-trapnell-lab/cicero-release") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) (propagated-inputs (modify-inputs (package-propagated-inputs r-cicero) (delete "r-monocle") (prepend r-monocle3)))))) (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-cistopic (package (name "r-cistopic") (version "2.1.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf")))) (build-system r-build-system) (propagated-inputs (list r-aucell r-data-table r-dplyr r-dosnow r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer r-s4vectors)) (home-page "https://github.com/aertslab/cisTopic") (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") (description "The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as @dfn{Latent Dirichlet Allocation} (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.") (license license:gpl3))) (define-public r-cistopic-next (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803") (revision "1")) (package (inherit r-cistopic) (name "r-cistopic-next") ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd ;; since the previous release is 2.1.0. Oh well. (version (git-version "0.3.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/aertslab/cisTopic") (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2")))) (properties `((upstream-name . 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It is also allowed to read a GDS file in parallel with multiple R processes supported by the package @code{parallel}.") (license license:lgpl3))) (define-public r-bigmelon (package (name "r-bigmelon") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-gdsfmt r-geoquery r-illuminaio r-methylumi r-minfi r-watermelon)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description "This package provides methods for working with Illumina arrays using the @code{gdsfmt} package.") (license license:gpl3))) (define-public r-seqbias (package (name "r-seqbias") (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicranges r-rhtslib)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.") 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