#:use-module (gnu packages compression)
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
+ #:use-module (gnu packages haskell)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
+\f
+;;; Annotations
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
based on mapping using Entrez Gene identifiers.")
(license license:artistic2.0)))
+(define-public r-org-hs-eg-db
+ (package
+ (name "r-org-hs-eg-db")
+ (version "3.7.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Hs.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
+ (properties
+ `((upstream-name . "org.Hs.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
+ (synopsis "Genome wide annotation for Human")
+ (description
+ "This package contains genome-wide annotations for Human, primarily based
+on mapping using Entrez Gene identifiers.")
+ (license license:artistic2.0)))
+
+(define-public r-org-mm-eg-db
+ (package
+ (name "r-org-mm-eg-db")
+ (version "3.7.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "org.Mm.eg.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
+ (properties
+ `((upstream-name . "org.Mm.eg.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
+ (synopsis "Genome wide annotation for Mouse")
+ (description
+ "This package provides mappings from Entrez gene identifiers to various
+annotations for the genome of the model mouse Mus musculus.")
+ (license license:artistic2.0)))
+
(define-public r-bsgenome-hsapiens-ucsc-hg19
(package
(name "r-bsgenome-hsapiens-ucsc-hg19")
(define-public r-genelendatabase
(package
(name "r-genelendatabase")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
"/geneLenDataBase_" version ".tar.gz"))
(sha256
(base32
- "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
+ "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
(properties
`((upstream-name . "geneLenDataBase")))
(build-system r-build-system)
based on the knownGene track.")
(license license:artistic2.0)))
+(define-public r-fdb-infiniummethylation-hg19
+ (package
+ (name "r-fdb-infiniummethylation-hg19")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "FDb.InfiniumMethylation.hg19_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
+ (properties
+ `((upstream-name . "FDb.InfiniumMethylation.hg19")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+ ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
+ (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
+ (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
+ (description
+ "This is an annotation package for Illumina Infinium DNA methylation
+probes. It contains the compiled HumanMethylation27 and HumanMethylation450
+annotations.")
+ (license license:artistic2.0)))
+
+(define-public r-illuminahumanmethylationepicmanifest
+ (package
+ (name "r-illuminahumanmethylationepicmanifest")
+ (version "0.3.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "IlluminaHumanMethylationEPICmanifest_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
+ (properties
+ `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-minfi" ,r-minfi)))
+ (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
+ (synopsis "Manifest for Illumina's EPIC methylation arrays")
+ (description
+ "This is a manifest package for Illumina's EPIC methylation arrays.")
+ (license license:artistic2.0)))
+
+(define-public r-do-db
+ (package
+ (name "r-do-db")
+ (version "2.9")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/annotation/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/annotation/src/contrib/"
+ "DO.db_" version ".tar.gz"))
+ (sha256
+ (base32
+ "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
+ (properties
+ `((upstream-name . "DO.db")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://www.bioconductor.org/packages/DO.db/")
+ (synopsis "Annotation maps describing the entire Disease Ontology")
+ (description
+ "This package provides a set of annotation maps describing the entire
+Disease Ontology.")
+ (license license:artistic2.0)))
+
+\f
+;;; Experiment data
+
+(define-public r-hsmmsinglecell
+ (package
+ (name "r-hsmmsinglecell")
+ (version "1.2.0")
+ (source (origin
+ (method url-fetch)
+ ;; We cannot use bioconductor-uri here because this tarball is
+ ;; located under "data/experiment/" instead of "bioc/".
+ (uri (string-append "https://www.bioconductor.org/packages/"
+ "release/data/experiment/src/contrib/"
+ "HSMMSingleCell_" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
+ (properties
+ `((upstream-name . "HSMMSingleCell")))
+ (build-system r-build-system)
+ (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
+ (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
+ (description
+ "Skeletal myoblasts undergo a well-characterized sequence of
+morphological and transcriptional changes during differentiation. In this
+experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
+under high mitogen conditions (GM) and then differentiated by switching to
+low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
+hundred cells taken over a time-course of serum-induced differentiation.
+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)))
+
\f
+;;; Packages
+
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.60.0")
+ (version "1.60.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
+ "0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
"This package provides functions for plotting genomic data.")
(license license:artistic2.0)))
+(define-public r-qvalue
+ (package
+ (name "r-qvalue")
+ (version "2.14.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "qvalue" version))
+ (sha256
+ (base32
+ "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-reshape2" ,r-reshape2)))
+ (home-page "http://github.com/jdstorey/qvalue")
+ (synopsis "Q-value estimation for false discovery rate control")
+ (description
+ "This package takes a list of p-values resulting from the simultaneous
+testing of many hypotheses and estimates their q-values and local @dfn{false
+discovery rate} (FDR) values. The q-value of a test measures the proportion
+of false positives incurred when that particular test is called significant.
+The local FDR measures the posterior probability the null hypothesis is true
+given the test's p-value. Various plots are automatically generated, allowing
+one to make sensible significance cut-offs. The software can be applied to
+problems in genomics, brain imaging, astrophysics, and data mining.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
(define-public r-diffbind
(package
(name "r-diffbind")
heuristics are used for model selection (i.e., to choose the number of
clusters).")
(license license:gpl3+)))
+
+(define-public r-deds
+ (package
+ (name "r-deds")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DEDS" version))
+ (sha256
+ (base32
+ "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
+ (properties `((upstream-name . "DEDS")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/DEDS/")
+ (synopsis "Differential expression via distance summary for microarray data")
+ (description
+ "This library contains functions that calculate various statistics of
+differential expression for microarray data, including t statistics, fold
+change, F statistics, SAM, moderated t and F statistics and B statistics. It
+also implements a new methodology called DEDS (Differential Expression via
+Distance Summary), which selects differentially expressed genes by integrating
+and summarizing a set of statistics using a weighted distance approach.")
+ ;; Any version of the LGPL.
+ (license license:lgpl3+)))
+
+;; This is a CRAN package, but since it depends on a Bioconductor package we
+;; put it here.
+(define-public r-nbpseq
+ (package
+ (name "r-nbpseq")
+ (version "0.3.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "NBPSeq" version))
+ (sha256
+ (base32
+ "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
+ (properties `((upstream-name . "NBPSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-qvalue" ,r-qvalue)))
+ (home-page "https://cran.r-project.org/web/packages/NBPSeq")
+ (synopsis "Negative binomial models for RNA-Seq data")
+ (description
+ "This package provides negative binomial models for two-group comparisons
+and regression inferences from RNA-sequencing data.")
+ (license license:gpl2)))
+
+(define-public r-ebseq
+ (package
+ (name "r-ebseq")
+ (version "1.22.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "EBSeq" version))
+ (sha256
+ (base32
+ "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
+ (properties `((upstream-name . "EBSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-blockmodeling" ,r-blockmodeling)
+ ("r-gplots" ,r-gplots)
+ ("r-testthat" ,r-testthat)))
+ (home-page "https://bioconductor.org/packages/EBSeq")
+ (synopsis "Differential expression analysis of RNA-seq data")
+ (description
+ "This package provides tools for differential expression analysis at both
+gene and isoform level using RNA-seq data")
+ (license license:artistic2.0)))
+
+(define-public r-lpsymphony
+ (package
+ (name "r-lpsymphony")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "lpsymphony" version))
+ (sha256
+ (base32
+ "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
+ (build-system r-build-system)
+ (inputs
+ `(("gfortran" ,gfortran)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "http://r-forge.r-project.org/projects/rsymphony")
+ (synopsis "Symphony integer linear programming solver in R")
+ (description
+ "This package was derived from Rsymphony. The package provides an R
+interface to SYMPHONY, a linear programming solver written in C++. The main
+difference between this package and Rsymphony is that it includes the solver
+source code, while Rsymphony expects to find header and library files on the
+users' system. Thus the intention of @code{lpsymphony} is to provide an easy
+to install interface to SYMPHONY.")
+ ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
+ ;; lpsimphony is released under the same terms.
+ (license license:epl1.0)))
+
+(define-public r-ihw
+ (package
+ (name "r-ihw")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "IHW" version))
+ (sha256
+ (base32
+ "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
+ (properties `((upstream-name . "IHW")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-fdrtool" ,r-fdrtool)
+ ("r-lpsymphony" ,r-lpsymphony)
+ ("r-slam" ,r-slam)))
+ (home-page "https://bioconductor.org/packages/IHW")
+ (synopsis "Independent hypothesis weighting")
+ (description
+ "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
+procedure that increases power compared to the method of Benjamini and
+Hochberg by assigning data-driven weights to each hypothesis. The input to
+IHW is a two-column table of p-values and covariates. The covariate can be
+any continuous-valued or categorical variable that is thought to be
+informative on the statistical properties of each hypothesis test, while it is
+independent of the p-value under the null hypothesis.")
+ (license license:artistic2.0)))
+
+(define-public r-icobra
+ (package
+ (name "r-icobra")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "iCOBRA" version))
+ (sha256
+ (base32
+ "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
+ (properties `((upstream-name . "iCOBRA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-dplyr" ,r-dplyr)
+ ("r-dt" ,r-dt)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-limma" ,r-limma)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rocr" ,r-rocr)
+ ("r-scales" ,r-scales)
+ ("r-shiny" ,r-shiny)
+ ("r-shinybs" ,r-shinybs)
+ ("r-shinydashboard" ,r-shinydashboard)
+ ("r-upsetr" ,r-upsetr)))
+ (home-page "https://bioconductor.org/packages/iCOBRA")
+ (synopsis "Comparison and visualization of ranking and assignment methods")
+ (description
+ "This package provides functions for calculation and visualization of
+performance metrics for evaluation of ranking and binary
+classification (assignment) methods. It also contains a Shiny application for
+interactive exploration of results.")
+ (license license:gpl2+)))
+
+(define-public r-mast
+ (package
+ (name "r-mast")
+ (version "1.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MAST" version))
+ (sha256
+ (base32
+ "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
+ (properties `((upstream-name . "MAST")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-plyr" ,r-plyr)
+ ("r-progress" ,r-progress)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://github.com/RGLab/MAST/")
+ (synopsis "Model-based analysis of single cell transcriptomics")
+ (description
+ "This package provides methods and models for handling zero-inflated
+single cell assay data.")
+ (license license:gpl2+)))
+
+(define-public r-monocle
+ (package
+ (name "r-monocle")
+ (version "2.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "monocle" version))
+ (sha256
+ (base32
+ "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocviews" ,r-biocviews)
+ ("r-cluster" ,r-cluster)
+ ("r-combinat" ,r-combinat)
+ ("r-ddrtree" ,r-ddrtree)
+ ("r-densityclust" ,r-densityclust)
+ ("r-dplyr" ,r-dplyr)
+ ("r-fastica" ,r-fastica)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hsmmsinglecell" ,r-hsmmsinglecell)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-limma" ,r-limma)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plyr" ,r-plyr)
+ ("r-proxy" ,r-proxy)
+ ("r-qlcmatrix" ,r-qlcmatrix)
+ ("r-rann" ,r-rann)
+ ("r-rcpp" ,r-rcpp)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rtsne" ,r-rtsne)
+ ("r-slam" ,r-slam)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-vgam" ,r-vgam)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://bioconductor.org/packages/monocle")
+ (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
+ (description
+ "Monocle performs differential expression and time-series analysis for
+single-cell expression experiments. It orders individual cells according to
+progress through a biological process, without knowing ahead of time which
+genes define progress through that process. Monocle also performs
+differential expression analysis, clustering, visualization, and other useful
+tasks on single cell expression data. It is designed to work with RNA-Seq and
+qPCR data, but could be used with other types as well.")
+ (license license:artistic2.0)))
+
+(define-public r-noiseq
+ (package
+ (name "r-noiseq")
+ (version "2.26.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "NOISeq" version))
+ (sha256
+ (base32
+ "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
+ (properties `((upstream-name . "NOISeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-matrix" ,r-matrix)))
+ (home-page "https://bioconductor.org/packages/NOISeq")
+ (synopsis "Exploratory analysis and differential expression for RNA-seq data")
+ (description
+ "This package provides tools to support the analysis of RNA-seq
+expression data or other similar kind of data. It provides exploratory plots
+to evaluate saturation, count distribution, expression per chromosome, type of
+detected features, features length, etc. It also supports the analysis of
+differential expression between two experimental conditions with no parametric
+assumptions.")
+ (license license:artistic2.0)))
+
+(define-public r-scdd
+ (package
+ (name "r-scdd")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scDD" version))
+ (sha256
+ (base32
+ "0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"))))
+ (properties `((upstream-name . "scDD")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-arm" ,r-arm)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-ebseq" ,r-ebseq)
+ ("r-fields" ,r-fields)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-mclust" ,r-mclust)
+ ("r-outliers" ,r-outliers)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scran" ,r-scran)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://github.com/kdkorthauer/scDD")
+ (synopsis "Mixture modeling of single-cell RNA-seq data")
+ (description
+ "This package implements a method to analyze single-cell RNA-seq data
+utilizing flexible Dirichlet Process mixture models. Genes with differential
+distributions of expression are classified into several interesting patterns
+of differences between two conditions. The package also includes functions
+for simulating data with these patterns from negative binomial
+distributions.")
+ (license license:gpl2)))
+
+(define-public r-scone
+ (package
+ (name "r-scone")
+ (version "1.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scone" version))
+ (sha256
+ (base32
+ "0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-aroma-light" ,r-aroma-light)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-boot" ,r-boot)
+ ("r-class" ,r-class)
+ ("r-cluster" ,r-cluster)
+ ("r-compositions" ,r-compositions)
+ ("r-diptest" ,r-diptest)
+ ("r-edger" ,r-edger)
+ ("r-fpc" ,r-fpc)
+ ("r-gplots" ,r-gplots)
+ ("r-hexbin" ,r-hexbin)
+ ("r-limma" ,r-limma)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-mixtools" ,r-mixtools)
+ ("r-rarpack" ,r-rarpack)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-ruvseq" ,r-ruvseq)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/scone")
+ (synopsis "Single cell overview of normalized expression data")
+ (description
+ "SCONE is an R package for comparing and ranking the performance of
+different normalization schemes for single-cell RNA-seq and other
+high-throughput analyses.")
+ (license license:artistic2.0)))
+
+(define-public r-geoquery
+ (package
+ (name "r-geoquery")
+ (version "2.50.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GEOquery" version))
+ (sha256
+ (base32
+ "074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"))))
+ (properties `((upstream-name . "GEOquery")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-dplyr" ,r-dplyr)
+ ("r-httr" ,r-httr)
+ ("r-limma" ,r-limma)
+ ("r-magrittr" ,r-magrittr)
+ ("r-readr" ,r-readr)
+ ("r-tidyr" ,r-tidyr)
+ ("r-xml2" ,r-xml2)))
+ (home-page "https://github.com/seandavi/GEOquery/")
+ (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
+ (description
+ "The NCBI Gene Expression Omnibus (GEO) is a public repository of
+microarray data. Given the rich and varied nature of this resource, it is
+only natural to want to apply BioConductor tools to these data. GEOquery is
+the bridge between GEO and BioConductor.")
+ (license license:gpl2)))
+
+(define-public r-illuminaio
+ (package
+ (name "r-illuminaio")
+ (version "0.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "illuminaio" version))
+ (sha256
+ (base32
+ "1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-base64" ,r-base64)))
+ (home-page "https://github.com/HenrikBengtsson/illuminaio/")
+ (synopsis "Parse Illumina microarray output files")
+ (description
+ "This package provides tools for parsing Illumina's microarray output
+files, including IDAT.")
+ (license license:gpl2)))
+
+(define-public r-siggenes
+ (package
+ (name "r-siggenes")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "siggenes" version))
+ (sha256
+ (base32
+ "0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-multtest" ,r-multtest)))
+ (home-page "https://bioconductor.org/packages/siggenes/")
+ (synopsis
+ "Multiple testing using SAM and Efron's empirical Bayes approaches")
+ (description
+ "This package provides tools for the identification of differentially
+expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
+both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
+Bayes Analyses of Microarrays} (EBAM).")
+ (license license:lgpl2.0+)))
+
+(define-public r-bumphunter
+ (package
+ (name "r-bumphunter")
+ (version "1.24.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bumphunter" version))
+ (sha256
+ (base32
+ "1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-dorng" ,r-dorng)
+ ("r-foreach" ,r-foreach)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-iterators" ,r-iterators)
+ ("r-limma" ,r-limma)
+ ("r-locfit" ,r-locfit)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/ririzarr/bumphunter")
+ (synopsis "Find bumps in genomic data")
+ (description
+ "This package provides tools for finding bumps in genomic data in order
+to identify differentially methylated regions in epigenetic epidemiology
+studies.")
+ (license license:artistic2.0)))
+
+(define-public r-minfi
+ (package
+ (name "r-minfi")
+ (version "1.28.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "minfi" version))
+ (sha256
+ (base32
+ "1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beanplot" ,r-beanplot)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bumphunter" ,r-bumphunter)
+ ("r-data-table" ,r-data-table)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-genefilter" ,r-genefilter)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-geoquery" ,r-geoquery)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-illuminaio" ,r-illuminaio)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-limma" ,r-limma)
+ ("r-mass" ,r-mass)
+ ("r-mclust" ,r-mclust)
+ ("r-nlme" ,r-nlme)
+ ("r-nor1mix" ,r-nor1mix)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape" ,r-reshape)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-siggenes" ,r-siggenes)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://github.com/hansenlab/minfi")
+ (synopsis "Analyze Illumina Infinium DNA methylation arrays")
+ (description
+ "This package provides tools to analyze and visualize Illumina Infinium
+methylation arrays.")
+ (license license:artistic2.0)))
+
+(define-public r-methylumi
+ (package
+ (name "r-methylumi")
+ (version "2.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "methylumi" version))
+ (sha256
+ (base32
+ "14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
+ ("r-genefilter" ,r-genefilter)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-illuminaio" ,r-illuminaio)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-minfi" ,r-minfi)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/methylumi")
+ (synopsis "Handle Illumina methylation data")
+ (description
+ "This package provides classes for holding and manipulating Illumina
+methylation data. Based on eSet, it can contain MIAME information, sample
+information, feature information, and multiple matrices of data. 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-lumi
+ (package
+ (name "r-lumi")
+ (version "2.34.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "lumi" version))
+ (sha256
+ (base32
+ "1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-affy" ,r-affy)
+ ("r-annotate" ,r-annotate)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-dbi" ,r-dbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-lattice" ,r-lattice)
+ ("r-mass" ,r-mass)
+ ("r-methylumi" ,r-methylumi)
+ ("r-mgcv" ,r-mgcv)
+ ("r-nleqslv" ,r-nleqslv)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-rsqlite" ,r-rsqlite)))
+ (home-page "https://bioconductor.org/packages/lumi")
+ (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
+ (description
+ "The lumi package provides an integrated solution for the Illumina
+microarray data analysis. It includes functions of Illumina
+BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
+variance stabilization, normalization and gene annotation at the probe level.
+It also includes the functions of processing Illumina methylation microarrays,
+especially Illumina Infinium methylation microarrays.")
+ (license license:lgpl2.0+)))
+
+(define-public r-linnorm
+ (package
+ (name "r-linnorm")
+ (version "2.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Linnorm" version))
+ (sha256
+ (base32
+ "1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"))))
+ (properties `((upstream-name . "Linnorm")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-amap" ,r-amap)
+ ("r-apcluster" ,r-apcluster)
+ ("r-ellipse" ,r-ellipse)
+ ("r-fastcluster" ,r-fastcluster)
+ ("r-fpc" ,r-fpc)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gmodels" ,r-gmodels)
+ ("r-igraph" ,r-igraph)
+ ("r-limma" ,r-limma)
+ ("r-mass" ,r-mass)
+ ("r-mclust" ,r-mclust)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcpparmadillo" ,r-rcpparmadillo)
+ ("r-rtsne" ,r-rtsne)
+ ("r-statmod" ,r-statmod)
+ ("r-vegan" ,r-vegan)
+ ("r-zoo" ,r-zoo)))
+ (home-page "http://www.jjwanglab.org/Linnorm/")
+ (synopsis "Linear model and normality based transformation method")
+ (description
+ "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
+count data or any large scale count data. It transforms such datasets for
+parametric tests. In addition to the transformtion function (@code{Linnorm}),
+the following pipelines are implemented:
+
+@enumerate
+@item Library size/batch effect normalization (@code{Linnorm.Norm})
+@item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
+ clustering or hierarchical clustering (@code{Linnorm.tSNE},
+ @code{Linnorm.PCA}, @code{Linnorm.HClust})
+@item Differential expression analysis or differential peak detection using
+ limma (@code{Linnorm.limma})
+@item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
+@item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
+@item Stable gene selection for scRNA-seq data; for users without or who do
+ not want to rely on spike-in genes (@code{Linnorm.SGenes})
+@item Data imputation (@code{Linnorm.DataImput}).
+@end enumerate
+
+Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
+@code{RnaXSim} function is included for simulating RNA-seq data for the
+evaluation of DEG analysis methods.")
+ (license license:expat)))
+
+(define-public r-ioniser
+ (package
+ (name "r-ioniser")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "IONiseR" version))
+ (sha256
+ (base32
+ "01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"))))
+ (properties `((upstream-name . "IONiseR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bit64" ,r-bit64)
+ ("r-dplyr" ,r-dplyr)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-shortread" ,r-shortread)
+ ("r-stringr" ,r-stringr)
+ ("r-tibble" ,r-tibble)
+ ("r-tidyr" ,r-tidyr)
+ ("r-xvector" ,r-xvector)))
+ (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 packages from Bioconductor.
+(define-public r-gkmsvm
+ (package
+ (name "r-gkmsvm")
+ (version "0.79.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gkmSVM" version))
+ (sha256
+ (base32
+ "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
+ (properties `((upstream-name . "gkmSVM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-kernlab" ,r-kernlab)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rocr" ,r-rocr)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)))
+ (home-page "https://cran.r-project.org/web/packages/gkmSVM")
+ (synopsis "Gapped-kmer support vector machine")
+ (description
+ "This R package provides tools for training gapped-kmer SVM classifiers
+for DNA and protein sequences. This package supports several sequence
+kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
+ (license license:gpl2+)))
+
+(define-public r-triform
+ (package
+ (name "r-triform")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "triform" version))
+ (sha256
+ (base32
+ "12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-iranges" ,r-iranges)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://bioconductor.org/packages/triform/")
+ (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
+ (description
+ "The Triform algorithm uses model-free statistics to identify peak-like
+distributions of TF ChIP sequencing reads, taking advantage of an improved
+peak definition in combination with known profile characteristics.")
+ (license license:gpl2)))
+
+(define-public r-varianttools
+ (package
+ (name "r-varianttools")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "VariantTools" version))
+ (sha256
+ (base32
+ "1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"))))
+ (properties `((upstream-name . "VariantTools")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-variantannotation" ,r-variantannotation)))
+ (home-page "https://bioconductor.org/packages/VariantTools/")
+ (synopsis "Tools for exploratory analysis of variant calls")
+ (description
+ "Explore, diagnose, and compare variant calls using filters. The
+VariantTools package supports a workflow for loading data, calling single
+sample variants and tumor-specific somatic mutations or other sample-specific
+variant types (e.g., RNA editing). Most of the functions operate on
+alignments (BAM files) or datasets of called variants. The user is expected
+to have already aligned the reads with a separate tool, e.g., GSNAP via
+gmapR.")
+ (license license:artistic2.0)))
+
+(define-public r-heatplus
+ (package
+ (name "r-heatplus")
+ (version "2.28.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Heatplus" version))
+ (sha256
+ (base32
+ "0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"))))
+ (properties `((upstream-name . "Heatplus")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "https://github.com/alexploner/Heatplus")
+ (synopsis "Heatmaps with row and/or column covariates and colored clusters")
+ (description
+ "This package provides tools to display a rectangular heatmap (intensity
+plot) of a data matrix. By default, both samples (columns) and features (row)
+of the matrix are sorted according to a hierarchical clustering, and the
+corresponding dendrogram is plotted. Optionally, panels with additional
+information about samples and features can be added to the plot.")
+ (license license:gpl2+)))
+
+(define-public r-gosemsim
+ (package
+ (name "r-gosemsim")
+ (version "2.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GOSemSim" version))
+ (sha256
+ (base32
+ "0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"))))
+ (properties `((upstream-name . "GOSemSim")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-go-db" ,r-go-db)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://guangchuangyu.github.io/software/GOSemSim")
+ (synopsis "GO-terms semantic similarity measures")
+ (description
+ "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
+quantitative ways to compute similarities between genes and gene groups, and
+have became important basis for many bioinformatics analysis approaches.
+GOSemSim is an R package for semantic similarity computation among GO terms,
+sets of GO terms, gene products and gene clusters.")
+ (license license:artistic2.0)))
+
+(define-public r-anota
+ (package
+ (name "r-anota")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "anota" version))
+ (sha256
+ (base32
+ "182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-multtest" ,r-multtest)
+ ("r-qvalue" ,r-qvalue)))
+ (home-page "https://bioconductor.org/packages/anota/")
+ (synopsis "Analysis of translational activity")
+ (description
+ "Genome wide studies of translational control is emerging as a tool to
+study verious biological conditions. The output from such analysis is both
+the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
+involved in translation (the actively translating mRNA level) for each mRNA.
+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 parallell the library performs a number of tests to assure that
+the data set is suitable for such analysis.")
+ (license license:gpl3)))
+
+(define-public r-sigpathway
+ (package
+ (name "r-sigpathway")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "sigPathway" version))
+ (sha256
+ (base32
+ "0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"))))
+ (properties `((upstream-name . "sigPathway")))
+ (build-system r-build-system)
+ (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
+ (synopsis "Pathway analysis")
+ (description
+ "This package is used to conduct pathway analysis by calculating the NT_k
+and NE_k statistics in a statistical framework for determining whether a
+specified group of genes for a pathway has a coordinated association with a
+phenotype of interest.")
+ (license license:gpl2)))
+
+(define-public r-fgsea
+ (package
+ (name "r-fgsea")
+ (version "1.8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fgsea" version))
+ (sha256
+ (base32
+ "0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-data-table" ,r-data-table)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/ctlab/fgsea/")
+ (synopsis "Fast gene set enrichment analysis")
+ (description
+ "The package implements an algorithm for fast gene set enrichment
+analysis. Using the fast algorithm allows to make more permutations and get
+more fine grained p-values, which allows to use accurate stantard approaches
+to multiple hypothesis correction.")
+ (license license:expat)))
+
+(define-public r-dose
+ (package
+ (name "r-dose")
+ (version "3.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DOSE" version))
+ (sha256
+ (base32
+ "1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"))))
+ (properties `((upstream-name . "DOSE")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-do-db" ,r-do-db)
+ ("r-fgsea" ,r-fgsea)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gosemsim" ,r-gosemsim)
+ ("r-qvalue" ,r-qvalue)
+ ("r-reshape2" ,r-reshape2)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://guangchuangyu.github.io/software/DOSE/")
+ (synopsis "Disease ontology semantic and enrichment analysis")
+ (description
+ "This package implements five methods proposed by Resnik, Schlicker,
+Jiang, Lin and Wang, respectively, for measuring semantic similarities among
+@dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
+including hypergeometric model and gene set enrichment analysis are also
+implemented for discovering disease associations of high-throughput biological
+data.")
+ (license license:artistic2.0)))
+
+(define-public r-enrichplot
+ (package
+ (name "r-enrichplot")
+ (version "1.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "enrichplot" version))
+ (sha256
+ (base32
+ "0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-cowplot" ,r-cowplot)
+ ("r-dose" ,r-dose)
+ ("r-europepmc" ,r-europepmc)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggplotify" ,r-ggplotify)
+ ("r-ggraph" ,r-ggraph)
+ ("r-ggridges" ,r-ggridges)
+ ("r-gosemsim" ,r-gosemsim)
+ ("r-gridextra" ,r-gridextra)
+ ("r-igraph" ,r-igraph)
+ ("r-purrr" ,r-purrr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape2" ,r-reshape2)
+ ("r-upsetr" ,r-upsetr)))
+ (home-page "https://github.com/GuangchuangYu/enrichplot")
+ (synopsis "Visualization of functional enrichment result")
+ (description
+ "The enrichplot package implements several visualization methods for
+interpreting functional enrichment results obtained from ORA or GSEA analyses.
+All the visualization methods are developed based on ggplot2 graphics.")
+ (license license:artistic2.0)))
+
+(define-public r-clusterprofiler
+ (package
+ (name "r-clusterprofiler")
+ (version "3.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "clusterProfiler" version))
+ (sha256
+ (base32
+ "1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"))))
+ (properties
+ `((upstream-name . "clusterProfiler")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-dose" ,r-dose)
+ ("r-enrichplot" ,r-enrichplot)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-go-db" ,r-go-db)
+ ("r-gosemsim" ,r-gosemsim)
+ ("r-magrittr" ,r-magrittr)
+ ("r-plyr" ,r-plyr)
+ ("r-qvalue" ,r-qvalue)
+ ("r-rvcheck" ,r-rvcheck)
+ ("r-tidyr" ,r-tidyr)))
+ (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
+ (synopsis "Analysis and visualization of functional profiles for gene clusters")
+ (description
+ "This package implements methods to analyze and visualize functional
+profiles (GO and KEGG) of gene and gene clusters.")
+ (license license:artistic2.0)))
+
+(define-public r-mlinterfaces
+ (package
+ (name "r-mlinterfaces")
+ (version "1.62.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MLInterfaces" version))
+ (sha256
+ (base32
+ "12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"))))
+ (properties `((upstream-name . "MLInterfaces")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotate" ,r-annotate)
+ ("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-cluster" ,r-cluster)
+ ("r-fpc" ,r-fpc)
+ ("r-gbm" ,r-gbm)
+ ("r-gdata" ,r-gdata)
+ ("r-genefilter" ,r-genefilter)
+ ("r-ggvis" ,r-ggvis)
+ ("r-hwriter" ,r-hwriter)
+ ("r-mass" ,r-mass)
+ ("r-mlbench" ,r-mlbench)
+ ("r-pls" ,r-pls)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rda" ,r-rda)
+ ("r-rpart" ,r-rpart)
+ ("r-sfsmisc" ,r-sfsmisc)
+ ("r-shiny" ,r-shiny)
+ ("r-threejs" ,r-threejs)))
+ (home-page "https://bioconductor.org/packages/MLInterfaces/")
+ (synopsis "Interfaces to R machine learning procedures")
+ (description
+ "This package provides uniform interfaces to machine learning code for
+data in R and Bioconductor containers.")
+ ;; Any version of the LGPL.
+ (license license:lgpl2.1+)))
+
+(define-public r-annaffy
+ (package
+ (name "r-annaffy")
+ (version "1.54.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "annaffy" version))
+ (sha256
+ (base32
+ "16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"))))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'remove-reference-to-non-free-data
+ (lambda _
+ (substitute* "DESCRIPTION"
+ ((", KEGG.db") ""))
+ #t)))))
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-dbi" ,r-dbi)
+ ("r-go-db" ,r-go-db)))
+ (home-page "https://bioconductor.org/packages/annaffy/")
+ (synopsis "Annotation tools for Affymetrix biological metadata")
+ (description
+ "This package provides functions for handling data from Bioconductor
+Affymetrix annotation data packages. It produces compact HTML and text
+reports including experimental data and URL links to many online databases.
+It allows searching of biological metadata using various criteria.")
+ ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
+ ;; the LGPL 2.1 is included.
+ (license license:lgpl2.1+)))
+
+(define-public r-a4core
+ (package
+ (name "r-a4core")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4Core" version))
+ (sha256
+ (base32
+ "1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"))))
+ (properties `((upstream-name . "a4Core")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-glmnet" ,r-glmnet)))
+ (home-page "https://bioconductor.org/packages/a4Core")
+ (synopsis "Automated Affymetrix array analysis core package")
+ (description
+ "This is the core package for the automated analysis of Affymetrix
+arrays.")
+ (license license:gpl3)))
+
+(define-public r-a4classif
+ (package
+ (name "r-a4classif")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4Classif" version))
+ (sha256
+ (base32
+ "02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"))))
+ (properties `((upstream-name . "a4Classif")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-a4core" ,r-a4core)
+ ("r-a4preproc" ,r-a4preproc)
+ ("r-glmnet" ,r-glmnet)
+ ("r-mlinterfaces" ,r-mlinterfaces)
+ ("r-pamr" ,r-pamr)
+ ("r-rocr" ,r-rocr)
+ ("r-varselrf" ,r-varselrf)))
+ (home-page "https://bioconductor.org/packages/a4Classif/")
+ (synopsis "Automated Affymetrix array analysis classification package")
+ (description
+ "This is the classification package for the automated analysis of
+Affymetrix arrays.")
+ (license license:gpl3)))
+
+(define-public r-a4preproc
+ (package
+ (name "r-a4preproc")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4Preproc" version))
+ (sha256
+ (base32
+ "1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"))))
+ (properties `((upstream-name . "a4Preproc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)))
+ (home-page "https://bioconductor.org/packages/a4Preproc/")
+ (synopsis "Automated Affymetrix array analysis preprocessing package")
+ (description
+ "This is a package for the automated analysis of Affymetrix arrays. It
+is used for preprocessing the arrays.")
+ (license license:gpl3)))
+
+(define-public r-a4reporting
+ (package
+ (name "r-a4reporting")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4Reporting" version))
+ (sha256
+ (base32
+ "124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"))))
+ (properties `((upstream-name . "a4Reporting")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annaffy" ,r-annaffy)
+ ("r-xtable" ,r-xtable)))
+ (home-page "https://bioconductor.org/packages/a4Reporting/")
+ (synopsis "Automated Affymetrix array analysis reporting package")
+ (description
+ "This is a package for the automated analysis of Affymetrix arrays. It
+provides reporting features.")
+ (license license:gpl3)))
+
+(define-public r-a4base
+ (package
+ (name "r-a4base")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4Base" version))
+ (sha256
+ (base32
+ "0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"))))
+ (properties `((upstream-name . "a4Base")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-a4core" ,r-a4core)
+ ("r-a4preproc" ,r-a4preproc)
+ ("r-annaffy" ,r-annaffy)
+ ("r-annotationdbi" ,r-annotationdbi)
+ ("r-biobase" ,r-biobase)
+ ("r-genefilter" ,r-genefilter)
+ ("r-glmnet" ,r-glmnet)
+ ("r-gplots" ,r-gplots)
+ ("r-limma" ,r-limma)
+ ("r-mpm" ,r-mpm)
+ ("r-multtest" ,r-multtest)))
+ (home-page "https://bioconductor.org/packages/a4Base/")
+ (synopsis "Automated Affymetrix array analysis base package")
+ (description
+ "This package provides basic features for the automated analysis of
+Affymetrix arrays.")
+ (license license:gpl3)))
+
+(define-public r-a4
+ (package
+ (name "r-a4")
+ (version "1.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "a4" version))
+ (sha256
+ (base32
+ "1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-a4base" ,r-a4base)
+ ("r-a4classif" ,r-a4classif)
+ ("r-a4core" ,r-a4core)
+ ("r-a4preproc" ,r-a4preproc)
+ ("r-a4reporting" ,r-a4reporting)))
+ (home-page "https://bioconductor.org/packages/a4/")
+ (synopsis "Automated Affymetrix array analysis umbrella package")
+ (description
+ "This package provides a software suite for the automated analysis of
+Affymetrix arrays.")
+ (license license:gpl3)))
+
+(define-public r-abseqr
+ (package
+ (name "r-abseqr")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "abseqR" version))
+ (sha256
+ (base32
+ "0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"))))
+ (properties `((upstream-name . "abseqR")))
+ (build-system r-build-system)
+ (inputs
+ `(("pandoc" ,ghc-pandoc)))
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-biocstyle" ,r-biocstyle)
+ ("r-circlize" ,r-circlize)
+ ("r-flexdashboard" ,r-flexdashboard)
+ ("r-ggcorrplot" ,r-ggcorrplot)
+ ("r-ggdendro" ,r-ggdendro)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-knitr" ,r-knitr)
+ ("r-plotly" ,r-plotly)
+ ("r-plyr" ,r-plyr)
+ ("r-png" ,r-png)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-stringr" ,r-stringr)
+ ("r-vegan" ,r-vegan)
+ ("r-venndiagram" ,r-venndiagram)))
+ (home-page "https://github.com/malhamdoosh/abseqR")
+ (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
+ (description
+ "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
+sequencing datasets generated from antibody libraries and abseqR is one of its
+packages. AbseqR empowers the users of abseqPy with plotting and reporting
+capabilities and allows them to generate interactive HTML reports for the
+convenience of viewing and sharing with other researchers. Additionally,
+abseqR extends abseqPy to compare multiple repertoire analyses and perform
+further downstream analysis on its output.")
+ (license license:gpl3)))
+
+(define-public r-bacon
+ (package
+ (name "r-bacon")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bacon" version))
+ (sha256
+ (base32
+ "1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-ellipse" ,r-ellipse)
+ ("r-ggplot2" ,r-ggplot2)))
+ (home-page "https://bioconductor.org/packages/bacon/")
+ (synopsis "Controlling bias and inflation in association studies")
+ (description
+ "Bacon can be used to remove inflation and bias often observed in
+epigenome- and transcriptome-wide association studies. To this end bacon
+constructs an empirical null distribution using a Gibbs Sampling algorithm by
+fitting a three-component normal mixture on z-scores.")
+ (license license:gpl2+)))
+
+(define-public r-rgadem
+ (package
+ (name "r-rgadem")
+ (version "2.30.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "rGADEM" version))
+ (sha256
+ (base32
+ "1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"))))
+ (properties `((upstream-name . "rGADEM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-iranges" ,r-iranges)
+ ("r-seqlogo" ,r-seqlogo)))
+ (home-page "https://bioconductor.org/packages/rGADEM/")
+ (synopsis "De novo sequence motif discovery")
+ (description
+ "rGADEM is an efficient de novo motif discovery tool for large-scale
+genomic sequence data.")
+ (license license:artistic2.0)))
+
+(define-public r-motiv
+ (package
+ (name "r-motiv")
+ (version "1.38.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "MotIV" version))
+ (sha256
+ (base32
+ "1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"))))
+ (properties `((upstream-name . "MotIV")))
+ (build-system r-build-system)
+ (inputs
+ `(("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-iranges" ,r-iranges)
+ ("r-lattice" ,r-lattice)
+ ("r-rgadem" ,r-rgadem)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/MotIV/")
+ (synopsis "Motif identification and validation")
+ (description
+ "This package is used for the identification and validation of sequence
+motifs. It makes use of STAMP for comparing a set of motifs to a given
+database (e.g. JASPAR). It can also be used to visualize motifs, motif
+distributions, modules and filter motifs.")
+ (license license:gpl2)))
+
+(define-public r-motifstack
+ (package
+ (name "r-motifstack")
+ (version "1.26.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "motifStack" version))
+ (sha256
+ (base32
+ "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"))))
+ (properties `((upstream-name . "motifStack")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ade4" ,r-ade4)
+ ("r-biostrings" ,r-biostrings)
+ ("r-grimport" ,r-grimport)
+ ("r-htmlwidgets" ,r-htmlwidgets)
+ ("r-motiv" ,r-motiv)
+ ("r-scales" ,r-scales)
+ ("r-xml" ,r-xml)))
+ (home-page "https://bioconductor.org/packages/motifStack/")
+ (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
+ (description
+ "The motifStack package is designed for graphic representation of
+multiple motifs with different similarity scores. It works with both DNA/RNA
+sequence motifs and amino acid sequence motifs. In addition, it provides the
+flexibility for users to customize the graphic parameters such as the font
+type and symbol colors.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff