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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 920 |
1 files changed, 920 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ea8a885c5f..25202410e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -40,6 +40,7 @@ #: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) @@ -84,6 +85,31 @@ submit gene-specific information, or which are scheduled for intense sequence analysis.") (license license:artistic2.0))) +(define-public r-org-bt-eg-db + (package + (name "r-org-bt-eg-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "org.Bt.eg.db" + version + 'annotation)) + (sha256 + (base32 + "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi")))) + (properties `((upstream-name . "org.Bt.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/org.Bt.eg.db") + (synopsis "Genome wide annotation for Bovine") + (description + "This package provides genome wide annotations for Bovine, primarily +based on mapping using Entrez Gene identifiers.") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") @@ -487,6 +513,34 @@ information about the latest version of the Gene Ontologies.") several related annotation packages.") (license license:artistic2.0))) +(define-public r-mus-musculus + (package + (name "r-mus-musculus") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Mus.musculus" version 'annotation)) + (sha256 + (base32 + "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y")))) + (properties `((upstream-name . "Mus.musculus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-mm-eg-db" ,r-org-mm-eg-db) + ("r-organismdbi" ,r-organismdbi) + ("r-txdb-mmusculus-ucsc-mm10-knowngene" + ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (home-page "https://bioconductor.org/packages/Mus.musculus") + (synopsis "Annotation package for the Mus.musculus object") + (description + "This package contains the @code{Mus.musculus} object to access data +from several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -1060,6 +1114,32 @@ sequencing data.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-biscuiteerdata + (package + (name "r-biscuiteerdata") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteerData" version 'experiment)) + (sha256 + (base32 + "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj")))) + (properties + `((upstream-name . "biscuiteerData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-curl" ,r-curl) + ("r-experimenthub" ,r-experimenthub))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biscuiteerData") + (synopsis "Data package for Biscuiteer") + (description + "This package contains default datasets used by the Bioconductor package +biscuiteer.") + (license license:gpl3))) + (define-public r-chromstardata (package (name "r-chromstardata") @@ -13733,6 +13813,846 @@ BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files.") (license license:artistic2.0))) +(define-public r-beclear + (package + (name "r-beclear") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BEclear" version)) + (sha256 + (base32 + "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + (properties `((upstream-name . "BEclear"))) + (build-system r-build-system) + (propagated-inputs + `(("r-abind" ,r-abind) + ("r-biocparallel" ,r-biocparallel) + ("r-data-table" ,r-data-table) + ("r-futile-logger" ,r-futile-logger) + ("r-matrix" ,r-matrix) + ("r-outliers" ,r-outliers) + ("r-rcpp" ,r-rcpp) + ("r-rdpack" ,r-rdpack))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/uds-helms/BEclear") + (synopsis "Correction of batch effects in DNA methylation data") + (description + "This package provides functions to detect and correct for batch effects +in DNA methylation data. The core function is based on latent factor models +and can also be used to predict missing values in any other matrix containing +real numbers.") + (license license:gpl3))) + +(define-public r-bgeecall + (package + (name "r-bgeecall") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeCall" version)) + (sha256 + (base32 + "1byciy7vzbdkdgaim10s9qb7zlxsywbhcsrka31gm0rm9ljqc665")))) + (properties `((upstream-name . "BgeeCall"))) + (build-system r-build-system) + (propagated-inputs + `(("kallisto" ,kallisto) + ("r-biomart" ,r-biomart) + ("r-biostrings" ,r-biostrings) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-jsonlite" ,r-jsonlite) + ("r-rhdf5" ,r-rhdf5) + ("r-rslurm" ,r-rslurm) + ("r-rtracklayer" ,r-rtracklayer) + ("r-sjmisc" ,r-sjmisc) + ("r-tximport" ,r-tximport))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/BgeeDB/BgeeCall") + (synopsis "RNA-Seq present/absent gene expression calls generation") + (description + "BgeeCall allows to generate present/absent gene expression calls without +using an arbitrary cutoff like TPM<1. Calls are generated based on reference +intergenic sequences. These sequences are generated based on expression of +all RNA-Seq libraries of each species integrated in Bgee.") + (license license:gpl3))) + +(define-public r-bgeedb + (package + (name "r-bgeedb") + (version "2.18.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeDB" version)) + (sha256 + (base32 + "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + (properties `((upstream-name . "BgeeDB"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-curl" ,r-curl) + ("r-data-table" ,r-data-table) + ("r-digest" ,r-digest) + ("r-dplyr" ,r-dplyr) + ("r-graph" ,r-graph) + ("r-r-utils" ,r-r-utils) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-tidyr" ,r-tidyr) + ("r-topgo" ,r-topgo))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/BgeeDB/BgeeDB_R") + (synopsis "Annotation and gene expression data retrieval from Bgee database") + (description + "This package provides a package for the annotation and gene expression +data download from Bgee database, and TopAnat analysis: GO-like enrichment of +anatomical terms, mapped to genes by expression patterns.") + (license license:gpl3))) + +(define-public r-biobtreer + (package + (name "r-biobtreer") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biobtreeR" version)) + (sha256 + (base32 + "0pynx4ps1qxsn13ba6zyg6h5dqlp2y7qish67m7sdjns079zh061")))) + (properties `((upstream-name . "biobtreeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-httr" ,r-httr) + ("r-jsonlite" ,r-jsonlite) + ("r-stringi" ,r-stringi))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tamerh/biobtreeR") + (synopsis "Use biobtree tool from R") + (description + "The biobtreeR package provides an interface to biobtree, a tool which +covers large sets of bioinformatics datasets and allows search and chain +mappings functionalities.") + (license license:expat))) + +(define-public r-minet + (package + (name "r-minet") + (version "3.50.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "minet" version)) + (sha256 + (base32 + "0bir2zr4r2wawkdvdhrk2hcyxmgkrkfvx36jj85fcm24axlqrzzb")))) + (properties `((upstream-name . "minet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-infotheo" ,r-infotheo))) + (home-page "http://minet.meyerp.com") + (synopsis "Mutual information networks") + (description + "This package implements various algorithms for inferring mutual +information networks from data.") + (license license:artistic2.0))) + +(define-public r-genetclassifier + (package + (name "r-genetclassifier") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "geNetClassifier" version)) + (sha256 + (base32 + "1i1cavbbvxzqgqxfmikghnls18jrq12hb953mjrwa95lkhzdxm2d")))) + (properties + `((upstream-name . "geNetClassifier"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-e1071" ,r-e1071) + ("r-ebarrays" ,r-ebarrays) + ("r-minet" ,r-minet))) + (home-page "https://www.cicancer.org") + (synopsis "Classify diseases and build gene networks using expression profiles") + (description + "This is a comprehensive package to automatically train and validate a +multi-class SVM classifier based on gene expression data. It provides +transparent selection of gene markers, their coexpression networks, and an +interface to query the classifier.") + (license license:gpl2+))) + +(define-public r-dir-expiry + (package + (name "r-dir-expiry") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dir.expiry" version)) + (sha256 + (base32 + "05mk7iwzay1xrgvssbz7nyl5d1n03syalbk18lmjmbx05dy0cjik")))) + (properties `((upstream-name . "dir.expiry"))) + (build-system r-build-system) + (propagated-inputs `(("r-filelock" ,r-filelock))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/dir.expiry") + (synopsis "Managing expiration for cache directories") + (description + "This package implements an expiration system for access to versioned +directories. Directories that have not been accessed by a registered function +within a certain time frame are deleted. This aims to reduce disk usage by +eliminating obsolete caches generated by old versions of packages.") + (license license:gpl3))) + +(define-public r-basilisk-utils + (package + (name "r-basilisk-utils") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "basilisk.utils" version)) + (sha256 + (base32 + "0qbm6rj6h059hakflbwz4j4f59311jhbk5dnpx11kyixh5pgjk7v")))) + (properties + `((upstream-name . "basilisk.utils"))) + (build-system r-build-system) + (propagated-inputs + `(("r-dir-expiry" ,r-dir-expiry))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/basilisk.utils") + (synopsis "Basilisk installation utilities") + (description + "This package implements utilities for installation of the basilisk +package, primarily for creation of the underlying Conda instance.") + (license license:gpl3))) + +(define-public r-basilisk + (package + (name "r-basilisk") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "basilisk" version)) + (sha256 + (base32 + "1nzbn3f2jzvg3a3m6wgksi4cvamqas2q7csdk4ir7fcirasf536v")))) + (properties `((upstream-name . "basilisk"))) + (build-system r-build-system) + (propagated-inputs + `(("r-basilisk-utils" ,r-basilisk-utils) + ("r-dir-expiry" ,r-dir-expiry) + ("r-reticulate" ,r-reticulate))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/basilisk") + (synopsis "Freeze Python dependencies inside Bioconductor packages") + (description + "This package installs a self-contained Conda instance that is managed by +the R/Bioconductor installation machinery. This aims to provide a consistent +Python environment that can be used reliably by Bioconductor packages. +Functions are also provided to enable smooth interoperability of multiple +Python environments in a single R session.") + (license license:gpl3))) + +(define-public r-biocthis + (package + (name "r-biocthis") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biocthis" version)) + (sha256 + (base32 + "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) + (properties `((upstream-name . "biocthis"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocmanager" ,r-biocmanager) + ("r-fs" ,r-fs) + ("r-glue" ,r-glue) + ("r-rlang" ,r-rlang) + ("r-styler" ,r-styler) + ("r-usethis" ,r-usethis))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/lcolladotor/biocthis") + (synopsis "Automate package and project setup for Bioconductor packages") + (description + "This package expands the @code{usethis} package with the goal of helping +automate the process of creating R packages for Bioconductor or making them +Bioconductor-friendly.") + (license license:artistic2.0))) + +(define-public r-biocdockermanager + (package + (name "r-biocdockermanager") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BiocDockerManager" version)) + (sha256 + (base32 + "0dh1flm5chsdcihljrg6znjskqkp0qyjh39hsv4zq0frf1rm97j7")))) + (properties + `((upstream-name . "BiocDockerManager"))) + (build-system r-build-system) + (propagated-inputs + `(("docker" ,docker) + ("r-dplyr" ,r-dplyr) + ("r-httr" ,r-httr) + ("r-memoise" ,r-memoise) + ("r-readr" ,r-readr) + ("r-whisker" ,r-whisker))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocDockerManager") + (synopsis "Access and manage Bioconductor Docker images") + (description + "This package works analogous to BiocManager but for Docker images. Use +the BiocDockerManager package to install and manage Docker images provided by +the Bioconductor project.") + (license license:artistic2.0))) + +(define-public r-biodb + (package + (name "r-biodb") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biodb" version)) + (sha256 + (base32 + "1apnbr5p619nsrhd2drm6arj69sw0wijv8ap7dfrndqkffrpbfmx")))) + (properties `((upstream-name . "biodb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-chk" ,r-chk) + ("r-jsonlite" ,r-jsonlite) + ("r-lgr" ,r-lgr) + ("r-lifecycle" ,r-lifecycle) + ("r-openssl" ,r-openssl) + ("r-plyr" ,r-plyr) + ("r-progress" ,r-progress) + ("r-r6" ,r-r6) + ("r-rappdirs" ,r-rappdirs) + ("r-rcpp" ,r-rcpp) + ("r-rcurl" ,r-rcurl) + ("r-rsqlite" ,r-rsqlite) + ("r-stringr" ,r-stringr) + ("r-testthat" ,r-testthat) + ("r-withr" ,r-withr) + ("r-xml" ,r-xml) + ("r-yaml" ,r-yaml))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biodb") + (synopsis "Library for connecting to chemical and biological databases") + (description + "The biodb package provides access to standard remote chemical and +biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local +database files (CSV, SQLite), with easy retrieval of entries, access to web +services, search of compounds by mass and/or name, and mass spectra matching +for LCMS and MSMS. Its architecture as a development framework facilitates +the development of new database connectors for local projects or inside +separate published packages.") + (license license:agpl3+))) + +(define-public r-biomformat + (package + (name "r-biomformat") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biomformat" version)) + (sha256 + (base32 + "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + (properties `((upstream-name . "biomformat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-rhdf5" ,r-rhdf5))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/joey711/biomformat/") + (synopsis "Interface package for the BIOM file format") + (description + "This is an R package for interfacing with the BIOM format. This package +includes basic tools for reading biom-format files, accessing and subsetting +data tables from a biom object (which is more complex than a single table), as +well as limited support for writing a biom-object back to a biom-format file. +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 "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MVCClass" version)) + (sha256 + (base32 + "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + (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.") + (license license:lgpl2.1+))) + +(define-public r-biomvcclass + (package + (name "r-biomvcclass") + (version "1.60.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioMVCClass" version)) + (sha256 + (base32 + "04pld93nffbci47dnf0awmcmhlfzv599ggcd7hvq78w41ac60qv8")))) + (properties `((upstream-name . "BioMVCClass"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-graph" ,r-graph) + ("r-mvcclass" ,r-mvcclass) + ("r-rgraphviz" ,r-rgraphviz))) + (home-page "https://bioconductor.org/packages/BioMVCClass") + (synopsis "Model-View-Controller (MVC) classes that use Biobase") + (description + "This package contains classes used in model-view-controller (MVC) +design.") + (license license:lgpl2.1+))) + +(define-public r-biomvrcns + (package + (name "r-biomvrcns") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biomvRCNS" version)) + (sha256 + (base32 + "0wyzj422smr4m9mswzn9inc1sn86pnia7jmd6k28nd2a7fjyrm16")))) + (properties `((upstream-name . "biomvRCNS"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomicranges" ,r-genomicranges) + ("r-gviz" ,r-gviz) + ("r-iranges" ,r-iranges) + ("r-mvtnorm" ,r-mvtnorm))) + (home-page "https://bioconductor.org/packages/biomvRCNS") + (synopsis "Copy number study and segmentation for multivariate biological data") + (description + "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one +homogeneous segmentation model are designed and implemented for segmentation +genomic data, with the aim of assisting in transcripts detection using high +throughput technology like RNA-seq or tiling array, and copy number analysis +using aCGH or sequencing.") + (license license:gpl2+))) + +(define-public r-bionero + (package + (name "r-bionero") + (version "1.0.4") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNERO" version)) + (sha256 + (base32 + "1yj0pavyfrj2gsvaj1dkgmznibm2appxjx9rk5qjslhslmm5b05b")))) + (properties `((upstream-name . "BioNERO"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-complexheatmap" ,r-complexheatmap) + ("r-deseq2" ,r-deseq2) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-genie3" ,r-genie3) + ("r-ggnetwork" ,r-ggnetwork) + ("r-ggnewscale" ,r-ggnewscale) + ("r-ggplot2" ,r-ggplot2) + ("r-ggpubr" ,r-ggpubr) + ("r-igraph" ,r-igraph) + ("r-intergraph" ,r-intergraph) + ("r-matrixstats" ,r-matrixstats) + ("r-minet" ,r-minet) + ("r-netrep" ,r-netrep) + ("r-networkd3" ,r-networkd3) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-reshape2" ,r-reshape2) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-sva" ,r-sva) + ("r-wgcna" ,r-wgcna))) + (native-inputs + `(("r-knitr" ,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. BioNERO can be used +to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) +from gene expression data. Additionally, it can be used to explore +topological properties of protein-protein interaction (PPI) networks. GCN +inference relies on the popular WGCNA algorithm. GRN inference is based on +the \"wisdom of the crowds\" principle, which consists in inferring GRNs with +multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average +rank for each interaction pair. As all steps of network analyses are included +in this package, BioNERO makes users avoid having to learn the syntaxes of +several packages and how to communicate between them. Finally, users can also +identify consensus modules across independent expression sets and calculate +intra and interspecies module preservation statistics between different +networks.") + (license license:gpl3))) + +(define-public r-bionet + (package + (name "r-bionet") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNet" version)) + (sha256 + (base32 + "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + (properties `((upstream-name . "BioNet"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-graph" ,r-graph) + ("r-igraph" ,r-igraph) + ("r-rbgl" ,r-rbgl))) + (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html") + (synopsis "Functional analysis of biological networks") + (description + "This package provides functions for the integrated analysis of +protein-protein interaction networks and the detection of functional modules. +Different datasets can be integrated into the network by assigning p-values of +statistical tests to the nodes of the network. E.g. p-values obtained from +the differential expression of the genes from an Affymetrix array are assigned +to the nodes of the network. By fitting a beta-uniform mixture model and +calculating scores from the p-values, overall scores of network regions can be +calculated and an integer linear programming algorithm identifies the maximum +scoring subnetwork.") + (license license:gpl2+))) + +(define-public r-bionetstat + (package + (name "r-bionetstat") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNetStat" version)) + (sha256 + (base32 + "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + (properties `((upstream-name . "BioNetStat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-knitr" ,r-knitr) + ("r-markdown" ,r-markdown) + ("r-pathview" ,r-pathview) + ("r-pheatmap" ,r-pheatmap) + ("r-plyr" ,r-plyr) + ("r-psych" ,r-psych) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rjsonio" ,r-rjsonio) + ("r-rmarkdown" ,r-rmarkdown) + ("r-shiny" ,r-shiny) + ("r-shinybs" ,r-shinybs) + ("r-whisker" ,r-whisker) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jardimViniciusC/BioNetStat") + (synopsis "Biological network analysis") + (description + "This package provides a package to perform differential network +analysis, differential node analysis (differential coexpression analysis), +network and metabolic pathways view.") + (license license:gpl3+))) + +(define-public r-bioqc + (package + (name "r-bioqc") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioQC" version)) + (sha256 + (base32 + "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l")))) + (properties `((upstream-name . "BioQC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edger" ,r-edger) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://accio.github.io/BioQC/") + (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") + (description + "BioQC performs quality control of high-throughput expression data based +on tissue gene signatures. It can detect tissue heterogeneity in gene +expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is +optimised for high performance.") + (license license:gpl3+))) + +(define-public r-biotip + (package + (name "r-biotip") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioTIP" version)) + (sha256 + (base32 + "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js")))) + (properties `((upstream-name . "BioTIP"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-mass" ,r-mass) + ("r-psych" ,r-psych) + ("r-stringr" ,r-stringr))) + (native-inputs + `(("r-knitr" ,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 "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biotmle" version)) + (sha256 + (base32 + "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f")))) + (properties `((upstream-name . "biotmle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-dofuture" ,r-dofuture) + ("r-dplyr" ,r-dplyr) + ("r-drtmle" ,r-drtmle) + ("r-future" ,r-future) + ("r-ggplot2" ,r-ggplot2) + ("r-ggsci" ,r-ggsci) + ("r-limma" ,r-limma) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-superheat" ,r-superheat) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://code.nimahejazi.org/biotmle/") + (synopsis "Targeted learning with moderated statistics for biomarker discovery") + (description + "This package provides tools for differential expression biomarker +discovery based on microarray and next-generation sequencing data that +leverage efficient semiparametric estimators of the average treatment effect +for variable importance analysis. Estimation and inference of the (marginal) +average treatment effects of potential biomarkers are computed by targeted +minimum loss-based estimation, with joint, stable inference constructed across +all biomarkers using a generalization of moderated statistics for use with the +estimated efficient influence function. The procedure accommodates the use of +ensemble machine learning for the estimation of nuisance functions.") + (license license:expat))) + +(define-public r-bsseq + (package + (name "r-bsseq") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bsseq" version)) + (sha256 + (base32 + "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + (properties `((upstream-name . "bsseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-hdf5array" ,r-hdf5array) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-permute" ,r-permute) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5" ,r-rhdf5) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/hansenlab/bsseq") + (synopsis "Analyze, manage and store bisulfite sequencing data") + (description + "This package provides a collection of tools for analyzing and +visualizing bisulfite sequencing data.") + (license license:artistic2.0))) + +(define-public r-dmrseq + (package + (name "r-dmrseq") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dmrseq" version)) + (sha256 + (base32 + "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + (properties `((upstream-name . "dmrseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-annotatr" ,r-annotatr) + ("r-biocparallel" ,r-biocparallel) + ("r-bsseq" ,r-bsseq) + ("r-bumphunter" ,r-bumphunter) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats) + ("r-nlme" ,r-nlme) + ("r-outliers" ,r-outliers) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/dmrseq") + (synopsis "Detection and inference of differentially methylated regions") + (description + "This package implements an approach for scanning the genome to detect +and perform accurate inference on differentially methylated regions from Whole +Genome Bisulfite Sequencing data. The method is based on comparing detected +regions to a pooled null distribution, that can be implemented even when as +few as two samples per population are available. Region-level statistics are +obtained by fitting a @dfn{generalized least squares} (GLS) regression model +with a nested autoregressive correlated error structure for the effect of +interest on transformed methylation proportions.") + (license license:expat))) + +(define-public r-biscuiteer + (package + (name "r-biscuiteer") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteer" version)) + (sha256 + (base32 + "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + (properties `((upstream-name . "biscuiteer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biscuiteerdata" ,r-biscuiteerdata) + ("r-bsseq" ,r-bsseq) + ("r-data-table" ,r-data-table) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dmrseq" ,r-dmrseq) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-hdf5array" ,r-hdf5array) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-impute" ,r-impute) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-mus-musculus" ,r-mus-musculus) + ("r-qdnaseq" ,r-qdnaseq) + ("r-qualv" ,r-qualv) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/trichelab/biscuiteer") + (synopsis "Convenience functions for the Biscuit package") + (description + "This package provides a test harness for bsseq loading of Biscuit +output, summarization of WGBS data over defined regions and in mappable +samples, with or without imputation, dropping of mostly-NA rows, age +estimates, etc.") + (license license:gpl3))) + (define-public r-tximeta (package (name "r-tximeta") |