;;; 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, 2022 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 autotools) #: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 java) #:use-module (gnu packages maths) #:use-module (gnu packages netpbm) #:use-module (gnu packages python) #: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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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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(define-public r-absfiltergsea (package (name "r-absfiltergsea") (version "1.5.1") (source (origin (method url-fetch) (uri (cran-uri "AbsFilterGSEA" version)) (sha256 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w")))) (properties `((upstream-name . "AbsFilterGSEA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo)) (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/") (synopsis "Improved false positive control of gene-permuting with absolute filtering") (description "This package provides a function that performs gene-permuting of a gene-set enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.") (license license:gpl2))) ;; This is a CRAN package, but it depends on r-biobase from Bioconductor. 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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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(license license:gpl3))) (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") (version "3.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg")))) (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-msnbase (package (name "r-msnbase") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3")))) (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.") 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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.") 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(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 . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-biobase r-biocgenerics r-biocmanager r-dbi r-genomicfeatures r-genomicranges r-graph r-iranges r-rbgl r-s4vectors)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.") (license license:artistic2.0))) (define-public r-pcaexplorer (package (name "r-pcaexplorer") (version "2.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-pcamethods (package (name "r-pcamethods") (version "1.88.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b")))) (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+))) ;; 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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(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).") 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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 "1.22.0") (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 "2.10.5") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2")))) (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.") (license license:artistic2.0))) (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) (propagated-inputs (list r-all r-biobase r-cluster)) (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") (synopsis "Clustering algorithm") (description "This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.") (license license:gpl2))) ;; This is the latest commit and it solves a bug from the latest release. (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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"flowViz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-flowcore r-hexbin r-idpmisc r-kernsmooth r-lattice r-latticeextra r-mass r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/flowViz/") (synopsis "Visualization for flow cytometry") (description "This package provides visualization tools for flow cytometry data.") (license license:artistic2.0))) (define-public r-flowclust (package (name "r-flowclust") (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk")))) (properties `((upstream-name . 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"flowWorkspace"))) (build-system r-build-system) (propagated-inputs (list r-aws-s3 r-aws-signature r-bh r-biobase r-biocgenerics r-cytolib r-data-table r-delayedarray r-digest r-dplyr r-flowcore r-ggplot2 r-graph r-lattice r-latticeextra r-matrixstats r-ncdfflow r-rbgl r-rcpp r-rcpparmadillo r-rcppparallel 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 "4.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc")))) (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 "2.8.4") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0")))) (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.") (license license:artistic2.0))) (define-public r-cytoml (package (name "r-cytoml") (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs (list libxml2 zlib)) (propagated-inputs (list r-base64enc r-bh r-biobase r-corpcor r-cytolib r-data-table r-dplyr r-flowcore r-flowworkspace r-ggcyto r-graph r-jsonlite r-lattice r-opencyto r-plyr r-rbgl r-rcpp r-rcpparmadillo r-rcppparallel r-rgraphviz r-rhdf5lib r-rprotobuflib r-runit r-tibble r-xml r-xml2 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 "2.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-colorramps r-consensusclusterplus r-cytoml r-dplyr r-flowcore r-flowworkspace r-ggforce r-ggnewscale r-ggplot2 r-ggpointdensity r-ggpubr r-ggrepel r-igraph r-magrittr r-pheatmap r-rcolorbrewer r-rlang r-rtsne r-scattermore 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 "6.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7")))) (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 "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp")))) (properties `((upstream-name . 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This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).") (license license:gpl3))) (define-public r-chicago (package (name "r-chicago") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm")))) (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). 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To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;