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-rw-r--r--gnu/packages/bioconductor.scm789
1 files changed, 789 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8df065a60c..251ad1e1ac 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -30,9 +30,13 @@
#:use-module (gnu packages gcc)
#:use-module (gnu packages graph)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
#:use-module (gnu packages web))
+
+;;; Annotations
+
(define-public r-bsgenome-celegans-ucsc-ce6
(package
(name "r-bsgenome-celegans-ucsc-ce6")
@@ -646,7 +650,103 @@ the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
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)))
+
+
+;;; 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)))
+
+;;; Packages
+
(define-public r-biocgenerics
(package
(name "r-biocgenerics")
@@ -766,6 +866,35 @@ region sets and other genomic features.")
"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")
@@ -1694,3 +1823,663 @@ estimation is performed using either the EM or CEM algorithm, and the slope
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)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-22 05:33:13 +0000