diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 789 |
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))) |