;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2024 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 . (define-module (gnu packages bioconductor) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix gexp) #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages chemistry) #: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 javascript) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #: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 protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module ((srfi srfi-1) #:hide (zip))) ;;; Annotations (define-public r-bsgenome-hsapiens-ucsc-hg38-masked (package (name "r-bsgenome-hsapiens-ucsc-hg38-masked") (version "1.4.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version 'annotation)) (sha256 (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m")))) (properties `((upstream-name . 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(license license:expat))) (define-public r-mousegastrulationdata (package (name "r-mousegastrulationdata") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MouseGastrulationData" version 'experiment)) (sha256 (base32 "0m03wrqgfhlyc0rmjjcj8b9gcc2rv644hffnff3j1bnkjg5rldi0")))) (properties `((upstream-name . "MouseGastrulationData"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-bumpymatrix r-experimenthub r-s4vectors r-singlecellexperiment r-spatialexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/MarioniLab/MouseGastrulationData") (synopsis "Single-Cell omics data across mouse gastrulation and early organogenesis") (description "This package provides processed and raw count data for single-cell RNA sequencing. 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Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the @code{MsExperiment} container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.") (license license:artistic2.0))) (define-public r-msigdb (package (name "r-msigdb") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msigdb" version 'experiment)) (sha256 (base32 "1fzgq31n059zhlkny3rfwfnriz81q9brk14r5yx2zhizlv8jcais")))) (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 "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALL" version 'experiment)) (sha256 (base32 "1ny5xv338a91gc88a1y5rrd27iawrrlmxhkidvc7xdsbrwd4flkc")))) (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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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 "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 "0av0kji4r788cn5808g13svqpydq6xk4d2awpzpsckz7xbjyx0ya")))) (properties `((upstream-name . 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This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.") (license license:expat))) (define-public r-derfinder (package (name "r-derfinder") (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinder" version)) (sha256 (base32 "0rj3szlpbxiwj3rajmr6ccnbs1mkcskql12iip8zgswmhz76rxh1")))) (properties `((upstream-name . 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It provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. It includes @code{GRanges} generation and plotting functions.") ;; GPLv3 with additional liability disclaimer. (license license:gpl3))) (define-public r-drimseq (package (name "r-drimseq") (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 (base32 "1nf044cfqywfnglm081xbppamva87z2j2xz0f51z8mra11apj6i6")))) (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. The package also makes available functions for visualization and exploration of the data and results.") (license license:gpl3+))) (define-public r-dropletutils (package (name "r-dropletutils") (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DropletUtils" version)) (sha256 (base32 "0bnxk72a0ygh4nqwyjzzi79zc4md8pwk0pr6jn43in0wdk054wf6")))) (properties `((upstream-name . 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(define-public r-dsb (package (name "r-dsb") (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "dsb" version)) (sha256 (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) (properties `((upstream-name . "dsb"))) (build-system r-build-system) (propagated-inputs (list r-limma r-magrittr r-mclust)) (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://github.com/niaid/dsb") (synopsis "Normalize & denoise droplet single cell protein data (CITE-Seq)") (description "R-dsb improves protein expression analysis in droplet-based single-cell studies. The package specifically addresses noise in raw protein UMI counts from methods like CITE-seq. It identifies and removes two main sources of noise—protein-specific noise from unbound antibodies and droplet/cell-specific noise. The package is applicable to various methods, including CITE-seq, REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb in Python.") (license license:cc0))) (define-public r-dss (package (name "r-dss") (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 "1wjd428kz2w3n4ak13h3i1yknm03fh911jrcy2hkcip4z5cssla0")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DSS") (synopsis "Dispersion shrinkage for sequencing data") (description "DSS is an R library performing differential analysis for count-based sequencing data. It detects @dfn{differentially expressed genes} (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from @dfn{bisulfite sequencing} (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) (define-public r-dyndoc (package (name "r-dyndoc") (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DynDoc" version)) (sha256 (base32 "0d2axaszy7rpi47yg4vhd1z70m53nx40znapgg5pq6ahrx7if5f1")))) (properties `((upstream-name . "DynDoc"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/DynDoc") (synopsis "Dynamic document tools") (description "This package provides a set of functions to create and interact with dynamic documents and vignettes.") 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A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells.") (license license:bsd-3))) (define-public r-iranges (package (name "r-iranges") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 "0rhh82hrsm32bdjamfah84p7zi8fvr4shyq2rdjfxzdp9qy5rh2q")))) (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 "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 (base32 "0zk9n94nqw6vpw908ka32zppxwqkki9krzxib06y1nic3bri3w9i")))) (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.") (license license:gpl2+))) ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-jetset (package (name "r-jetset") (version "3.4.0") (source (origin (method url-fetch) (uri (cran-uri "jetset" version)) (sha256 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp")))) (properties `((upstream-name . "jetset"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-org-hs-eg-db)) (home-page "http://www.cbs.dtu.dk/biotools/jetset/") (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays") (description "This package provides a one-to-one mapping from gene to \"best\" probe set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a, hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single gene may be measured by multiple probe sets. This can present a mild conundrum when attempting to evaluate a gene \"signature\" that is defined by gene names rather than by specific probe sets. This package also includes the pre-calculated probe set quality scores that were used to define the mapping.") (license license:artistic2.0))) (define-public r-nebulosa (package (name "r-nebulosa") (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Nebulosa" version)) (sha256 (base32 "11wn6l27cshhb1djsgqaqr8d33j4bipy0w0gafp3fkvg7mnpnhps")))) (properties `((upstream-name . "Nebulosa"))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-ggrastr r-ks r-matrix r-patchwork r-seuratobject r-singlecellexperiment r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://github.com/powellgenomicslab/Nebulosa") (synopsis "Single-cell data visualisation using kernel gene-weighted density estimation") (description "This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment} objects can be used within Nebulosa.") (license license:gpl3))) ;; This is a CRAN package but it requires r-rcy3, a Bioconductor package. (define-public r-netgsa (package (name "r-netgsa") (version "4.0.5") (source (origin (method url-fetch) (uri (cran-uri "netgsa" version)) (sha256 (base32 "1m9myxsbvbljr038azxzakpbh20a21qhiy20d0ipvjc5asq3kfla")))) (properties `((upstream-name . "netgsa"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-corpcor r-data-table r-dplyr r-genefilter r-glassofast r-glmnet r-graph r-graphite r-httr r-igraph r-magrittr r-matrix r-msigdbr r-org-hs-eg-db r-quadprog r-rcpp r-rcppeigen r-rcy3 r-reshape2 r-rlang)) (native-inputs (list r-knitr)) (home-page "https://github.com/mikehellstern/netgsa") (synopsis "Network-Based gene set analysis") (description "This package lets you carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. It implements methods described in Shojaie A, Michailidis G (2010) , Shojaie A, Michailidis G (2009) , and Ma J, Shojaie A, Michailidis G (2016) .") (license license:gpl3+))) ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package (name "r-nmf") (version "0.27") (source (origin (method url-fetch) (uri (cran-uri "NMF" version)) (sha256 (base32 "1y9y7xpfd9y8j5b8s2x5g61455ilpgqpdhrirpz58xjarbph4hxg")))) (properties `((upstream-name . "NMF"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocmanager r-bigmemory ;suggested r-cluster r-codetools r-colorspace r-digest r-doparallel r-foreach r-ggplot2 r-gridbase r-rcolorbrewer r-registry r-reshape2 r-rngtools r-stringr r-synchronicity)) ;suggested (native-inputs (list r-knitr)) (home-page "https://renozao.github.io/NMF") (synopsis "Algorithms and framework for nonnegative matrix factorization") (description "This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.") (license license:gpl2+))) (define-public r-affy (package (name "r-affy") (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 "0lsvcv7nprmsh62d0r2v44a5n915crvv1cbj9ba6fdggj7wp8zyk")))) (build-system r-build-system) (propagated-inputs (list r-affyio r-biobase r-biocgenerics r-biocmanager r-preprocesscore r-zlibbioc)) (inputs (list zlib)) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description "This package contains functions for exploratory oligonucleotide array analysis.") (license license:lgpl2.0+))) (define-public r-affycomp (package (name "r-affycomp") (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 "0818mgwny9hznw7lawrvmk11nwy0wxgjnlkf083vv3js4aq31gfp")))) (properties `((upstream-name . 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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 "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 "0y8nk9jq0z48phg13mf6hsfg8l54w6z6b67g0k1c9gmsb7aqq04d")))) (properties `((upstream-name . 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In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.") (license license:gpl2+))) (define-public r-methylkit (package (name "r-methylkit") (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 "0y45wa45kblm2g3nylvybvyfc34sjlynhsz3dirhs1favb83sdiv")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-mfuzz (package (name "r-mfuzz") (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Mfuzz" version)) (sha256 (base32 "0v2l3fi9331lxfam6az265rfk52g4n75hh4rg12ykhp86ihplzpf")))) (properties `((upstream-name . "Mfuzz"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) (home-page "http://mfuzz.sysbiolab.eu/") (synopsis "Soft clustering of time series gene expression data") (description "This is a package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).") (license license:gpl2))) (define-public r-mmuphin (package (name "r-mmuphin") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 (base32 "0lhvsx5yjvqh5d3h860sv8cf3h73nrzvljpkqrd9ks0irc4gcm6d")) ;; 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-modstrings (package (name "r-modstrings") (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Modstrings" version)) (sha256 (base32 "1jjawwkvdx02ss2vw4ah2b8psgxr01z6r1rkr2pnkmrp2ma7ygks")))) (properties `((upstream-name . 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In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.") (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 . "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.") 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(license license:gpl3))) (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") (version "3.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 "19ya4ax6pa727hdn0118l9pwa9dxgh89dz54mm66dawxga3jhar4")))) (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.") 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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 "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 "1rgkd9iv0lxj1zxh96sifwa312ivw5kl5jw82ma4fmapr4iqhzsh")))) (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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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 . 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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 "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 "1s55fiqgxrdznn43qhm5yv9gp8d1msr2f39wxih0b5bm4wxhkq45")))) (properties `((upstream-name . 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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 "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 (base32 "0pby2h8m12xlngpk33dvh3nkrpgqi4f2mb7g9jafyiv3sl8pjd19")))) (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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This package supports the independent phyloseq data format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.") (license license:bsd-2))) ;; This is a CRAN package but it depends on phyloseq, which is from ;; Bioconductor. (define-public r-microbiomestat (package (name "r-microbiomestat") (version "1.1") (source (origin (method url-fetch) (uri (cran-uri "MicrobiomeStat" version)) (sha256 (base32 "1j5sar85a1gksc83pc4ypxwb0c7whxglx069zarphrgqfazcr1m4")))) (properties `((upstream-name . 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The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.") 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An \"intelligent\" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) (define-public r-lefser (package (name "r-lefser") (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "lefser" version)) (sha256 (base32 "0aywwinp4wwwa12rq60gpfk5gn28zyimayxakgj4lhfwjk0byz8m")))) (properties `((upstream-name . 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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 "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 "1y595hq40kpsasp74wsbf3ngd2rrriqg65z9y4svcwdygj03pgrz")))) (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 "1.9") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 "1w4mv7vb94d4pkllvabz9az8sbrbfhigxw4is3j0jzi1pnlyc8kg")))) (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.") 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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.") 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The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e., differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.") (license license:gpl3))) (define-public r-anota2seq (package (name "r-anota2seq") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota2seq" version)) (sha256 (base32 "0kyxwhj5vq5z4v3x3hfb9ks3h37axqskyj9rzyj2bzsy2yk9hajn")))) (properties `((upstream-name . 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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 "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 "16nkxnbsmr0y6km794x2iwbkyrkf0svg6ln3qkqnw0a47a3cbm65")))) (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 "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 "0rgfl1kmgf2f0lpj2fzgjvdm5d7swp9wz86jl8q9mydw6z49nxz8")))) (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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(define-public r-cytolib (package (name "r-cytolib") (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 "1kagik93ddcl3m1i2bqzzlh18lbxywfn3pxmp47p45kayzxzldrf")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (inputs (list openblas protobuf zlib)) (native-inputs (list r-knitr)) (propagated-inputs (list r-bh r-rhdf5lib r-rprotobuflib)) (home-page "https://bioconductor.org/packages/cytolib/") (synopsis "C++ infrastructure for working with gated cytometry") (description "This package provides the core data structure and API to represent and interact with gated cytometry data.") (license license:artistic2.0))) (define-public r-flowcore (package (name "r-flowcore") (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 "1g6qxzvzn1gnmqba150lj9nb6wlrdpzkc61l77d3fkzaf0q1h1n7")))) (properties `((upstream-name . 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(license license:artistic2.0))) (define-public r-flowstats (package (name "r-flowstats") (version "4.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 "1q4m6arasq60w0x24qjxbfckfgcpfk428fca733i0q2mgv1mll05")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-clue 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 "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 "12b4a65zgswzddkfdyl4j06qp7w9lkxv4h05m4z8hfff8c9x5bls")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics r-cpp11 r-data-table r-flowclust r-flowcore r-flowviz r-flowworkspace r-graph r-ncdfflow r-rbgl r-rcolorbrewer)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/openCyto") (synopsis "Hierarchical gating pipeline for flow cytometry data") (description "This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.") 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(license license:artistic2.0))) (define-public r-flowsom (package (name "r-flowsom") (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 "170xz3b4kfsxpqirfz9vk4j8dkdmz4qd0a1nm3yaya1rddpg9m3l")))) (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 "6.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 "0ifi89s611kblncnpvsrbl6sq2zi36binz63njrhya9wkyaxj6pc")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-corpcor r-dplyr r-ellipse r-ggplot2 r-ggrepel 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 "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 "1b3c1wg5xnhh4bdcjls26j6nsp0vx1g5y3grqv7x4ds01vmh3q2w")))) (properties `((upstream-name . 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As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) (define-public r-rcistarget (package (name "r-rcistarget") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 "0dp2y85mfn995rvg698xnxlkz1kd8g0byjypxx62cpfldnkrinxl")))) (properties `((upstream-name . 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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 "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 "1mcpx785ag0jcsh08df34hx3wp55zd1vggnl3fflkinb78178n38")))) (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 . "CIARA"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr)) (native-inputs (list r-knitr)) (home-page "https://cran.r-project.org/package=CIARA") (synopsis "Cluster-independent algorithm for rare cell types identification") (description "This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.") (license license:artistic2.0))) (define-public r-cicero (package (name "r-cicero") (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 "19vn31w74r45pq5m9pn5db1sz1qg757mghzzs933cdssnqf4m6y5")))) (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 "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 "098fbrszph5cnh4n9zjhj92sg1bi6h6k57wm2vlaqkq0nab63r63")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) (propagated-inputs (list r-annotationhub r-biostrings r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-deseq2 r-dplyr r-edger r-genomeinfodb r-genomicranges r-ggplot2 r-gwascat r-iranges r-magrittr r-r-utils r-readr r-reshape2 r-rlang r-rtracklayer r-s4vectors r-seqinr r-stringi r-stringr r-universalmotif)) (native-inputs (list r-knitr)) (home-page "https://github.com/Aufiero/circRNAprofiler") (synopsis "Computational framework for the downstream analysis of circular RNA's") (description "@code{r-circrnaprofiler} is a computational framework for a comprehensive in silico analysis of @dfn{circular RNA} (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.") (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 . "cisTopic"))) (propagated-inputs (list r-aucell r-data-table r-dosnow r-dplyr r-dt r-feather r-fitdistrplus r-genomicranges r-ggplot2 r-lda r-matrix r-plyr r-rcistarget r-rtracklayer r-s4vectors r-text2vec)) (native-inputs (list r-knitr))))) (define-public r-genie3 (package (name "r-genie3") (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 "0bsid8qhcqgalqghr2b2592pzm4viyi7wq8h5dmhrrl7gky8l60k")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs (list r-dplyr r-reshape2)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GENIE3") (synopsis "Gene network inference with ensemble of trees") (description "This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.") (license license:gpl2+))) (define-public r-roc (package (name "r-roc") (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 "12msc6skvcx4ajk20l71k32rj8lsiafjxwcsrd51kyy5x2yj2v4m")))) (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 "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 "1ra21qzni9cny52ag9zxi46vb9grabyqjyk01dqqp3r9i0b4999l")))) (properties `((upstream-name . 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(license license:gpl3))) (define-public r-gdsfmt (package (name "r-gdsfmt") (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 "03qgiww523kijrkciln3fw3djn20rnvwz2j0i3p518h6fbl7vlpm")) (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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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 "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 "1j80f7k39p23s6fym3nia73g8d1v44hdiv73igcq6fnsllxg40hr")))) (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 "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 "18pdpi855y1hhka96xc5886nqffjn1jhz9jr9p305iikdrsvmjp1")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs (list r-biostrings r-genomicranges r-rhtslib r-zlibbioc)) (home-page "https://bioconductor.org/packages/seqbias/") (synopsis "Estimation of per-position bias in high-throughput sequencing data") (description "This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.") (license license:lgpl3))) (define-public r-reqon (package (name "r-reqon") (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 "0w28b3ma8r8rshijdm5jj1z64v91my7hcvw18r9pdwjprh05bw0g")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs (list r-rjava r-rsamtools r-seqbias)) (home-page "https://bioconductor.org/packages/ReQON/") (synopsis "Recalibrating quality of nucleotides") (description "This package provides an implementation of an algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.") (license license:gpl2))) (define-public r-wavcluster (package (name "r-wavcluster") (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 "1y2bk1kla0l72xgdam2l9c0k7584ckdqscqnc184cxvqm6fb335j")))) (properties `((upstream-name . 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In addition, the package integrates RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) (define-public r-tilingarray (package (name "r-tilingarray") (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 "01j4wj0mdfrlyhp2alf1xfy78f17x43w9i0wb41ljw6pm313np58")))) (properties `((upstream-name . 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The main functionalities of the package are: @enumerate @item the class segmentation for representing partitionings of a linear series of data; @item the function segment for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; @item the function @code{confint} for calculating confidence intervals using the @code{strucchange} package; @item the function @code{plotAlongChrom} for generating pretty plots; @item the function @code{normalizeByReference} for probe-sequence dependent response adjustment from a (set of) reference hybridizations. @end enumerate") (license license:artistic2.0))) (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TimeSeriesExperiment" version)) (sha256 (base32 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c")))) (properties `((upstream-name . 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(license license:gpl2+))) (define-public r-htqpcr (package (name "r-htqpcr") (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 "14cff36ikbqhd5xizihpxzsv9jimcpbgnd381jd154pgi60bil0m")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer)) (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" "groups/bertone/software/HTqPCR.pdf")) (synopsis "Automated analysis of high-throughput qPCR data") (description "Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. 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The design of this API is intended to match the Python API and other tools included with the biom-format project, but with a decidedly \"R flavor\" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.") (license license:gpl2))) (define-public r-mvcclass (package (name "r-mvcclass") (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 "16finp6q89n6x5q2v1khpfp5ys7d4dvlh3kacv5qbdh1bsb3fpax")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") (synopsis "Model-View-Controller (MVC) classes") (description "This package contains classes used in model-view-controller (MVC) design.") 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(license license:gpl2+))) (define-public r-bionero (package (name "r-bionero") (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 "0dxn4pijr6gsqybl8x3ix1xydizg7gzfp72risk37zc5i4xk2lca")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-complexheatmap r-dynamictreecut r-genie3 r-ggdendro r-ggnetwork r-ggplot2 r-ggrepel r-igraph r-intergraph r-matrixstats r-minet r-netrep r-patchwork r-rcolorbrewer r-reshape2 r-rlang r-summarizedexperiment r-sva r-wgcna)) (native-inputs (list r-knitr)) (home-page "https://github.com/almeidasilvaf/BioNERO") (synopsis "Biological network reconstruction omnibus") (description "BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. 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(license license:gpl3+))) (define-public r-biotip (package (name "r-biotip") (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 "1bbjfv3bi20xlk8h7r5ipav6mfs27lmj0zjb5mk1gmp071dmnk0y")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs (list r-cluster r-genomicranges r-igraph r-mass r-psych r-scran r-stringr)) (native-inputs (list r-knitr)) (home-page "https://github.com/xyang2uchicago/BioTIP") (synopsis "R package for characterization of biological tipping-point") (description "This package adopts tipping-point theory to transcriptome profiles to help unravel disease regulatory trajectory.") (license license:gpl2))) (define-public r-biotmle (package (name "r-biotmle") (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 "0h796sxv7fvwx9m8ikamf3bvaac7rimp33lv1j3ngsjifigdkvfy")))) (properties `((upstream-name . 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Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.") (license license:lgpl2.0))) (define-public r-dmrseq (package (name "r-dmrseq") (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 "10ps9k5cp2adpx91g23gc9hl1qzzax5w1mxjcjaii7knkh70cz3p")))) (properties `((upstream-name . 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(license license:gpl3+))) (define-public r-tricycle (package (name "r-tricycle") (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 "1dawkp681pz9hf7fp2nag9pcfxx5rq0z4j9czlalf0sylsjbirkd")))) (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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To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar ;;; functionality or similar names. ;;;