;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
+;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
fitting of some classes of graphical Markov models.")
(license license:gpl2+)))
+;; This is a CRAN package, but it depends on a Bioconductor package.
(define-public r-codedepends
(package
(name "r-codedepends")
(define-public r-mixomics
(package
(name "r-mixomics")
- (version "6.12.1")
+ (version "6.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
- "13kq9l5xwhwp30y5gfqfh5f11n63vn8rk195mb2y2mww4cwi6lv4"))))
+ "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cicero
(package
(name "r-cicero")
- (version "1.6.1")
+ (version "1.6.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "cicero" version))
(sha256
(base32
- "0nf9yqg5krj26n4n82iyx3rsr84d46b17i9zfk35sh12l4xssbii"))))
+ "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
(build-system r-build-system)
(propagated-inputs
`(("r-assertthat" ,r-assertthat)
(define-public r-activedriverwgs
(package
(name "r-activedriverwgs")
- (version "1.0.1")
+ (version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActiveDriverWGS" version))
(sha256
(base32
- "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
+ "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
(properties
`((upstream-name . "ActiveDriverWGS")))
(build-system r-build-system)
("r-genomeinfodb" ,r-genomeinfodb)
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
- ("r-plyr" ,r-plyr)
("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
(home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
(synopsis "Driver discovery tool for cancer whole genomes")
(description
simulation to eliminate overestimation of @code{K} and can reject the null
hypothesis @code{K=1}.")
(license license:agpl3+)))
+
+(define-public r-icens
+ (package
+ (name "r-icens")
+ (version "1.60.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Icens" version))
+ (sha256
+ (base32
+ "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
+ (properties `((upstream-name . "Icens")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-survival" ,r-survival)))
+ (home-page "https://bioconductor.org/packages/Icens")
+ (synopsis "NPMLE for censored and truncated data")
+ (description
+ "This package provides many functions for computing the
+@dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
+truncated data.")
+ (license license:artistic2.0)))
+
+;; This is a CRAN package but it depends on r-icens, which is published on
+;; Bioconductor.
+(define-public r-interval
+ (package
+ (name "r-interval")
+ (version "1.1-0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "interval" version))
+ (sha256
+ (base32
+ "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
+ (properties `((upstream-name . "interval")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-icens" ,r-icens)
+ ("r-mlecens" ,r-mlecens)
+ ("r-perm" ,r-perm)
+ ("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/interval/")
+ (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
+ (description
+ "This package provides functions to fit nonparametric survival curves,
+plot them, and perform logrank or Wilcoxon type tests.")
+ (license license:gpl2+)))
+
+;; This is a CRAN package, but it depends on r-interval, which depends on a
+;; Bioconductor package.
+(define-public r-fhtest
+ (package
+ (name "r-fhtest")
+ (version "1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "FHtest" version))
+ (sha256
+ (base32
+ "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
+ (properties `((upstream-name . "FHtest")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-interval" ,r-interval)
+ ("r-kmsurv" ,r-kmsurv)
+ ("r-mass" ,r-mass)
+ ("r-perm" ,r-perm)
+ ("r-survival" ,r-survival)))
+ (home-page "https://cran.r-project.org/web/packages/FHtest/")
+ (synopsis "Tests for survival data based on the Fleming-Harrington class")
+ (description
+ "This package provides functions to compare two or more survival curves
+with:
+
+@itemize
+@item The Fleming-Harrington test for right-censored data based on
+ permutations and on counting processes.
+@item An extension of the Fleming-Harrington test for interval-censored data
+ based on a permutation distribution and on a score vector distribution.
+@end itemize
+")
+ (license license:gpl2+)))
+
+(define-public r-fourcseq
+ (package
+ (name "r-fourcseq")
+ (version "1.22.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FourCSeq" version))
+ (sha256
+ (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
+ (properties `((upstream-name . "FourCSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biostrings" ,r-biostrings)
+ ("r-deseq2" ,r-deseq2)
+ ("r-fda" ,r-fda)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gtools" ,r-gtools)
+ ("r-lsd" ,r-lsd)
+ ("r-matrix" ,r-matrix)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+ (synopsis "Analysis of multiplexed 4C sequencing data")
+ (description
+ "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions. The statistical analysis in R starts with individual bam
+files for each sample as inputs. To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences. With
+a standard alignment software the required bam files can be then be
+generated.")
+ (license license:gpl3+)))
+
+(define-public r-preprocesscore
+ (package
+ (name "r-preprocesscore")
+ (version "1.50.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "preprocessCore" version))
+ (sha256
+ (base32
+ "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
+ (properties
+ `((upstream-name . "preprocessCore")))
+ (build-system r-build-system)
+ (home-page "https://github.com/bmbolstad/preprocessCore")
+ (synopsis "Collection of pre-processing functions")
+ (description
+ "This package provides a library of core pre-processing and normalization
+routines.")
+ (license license:lgpl2.0+)))
+
+;; This is a CRAN package, but it depends on preprocessorcore, which is a
+;; Bioconductor package.
+(define-public r-wgcna
+ (package
+ (name "r-wgcna")
+ (version "1.69")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "WGCNA" version))
+ (sha256
+ (base32
+ "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
+ (properties `((upstream-name . "WGCNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-fastcluster" ,r-fastcluster)
+ ("r-foreach" ,r-foreach)
+ ("r-go-db" ,r-go-db)
+ ("r-hmisc" ,r-hmisc)
+ ("r-impute" ,r-impute)
+ ("r-rcpp" ,r-rcpp)
+ ("r-survival" ,r-survival)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-preprocesscore" ,r-preprocesscore)))
+ (home-page
+ "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
+ (synopsis "Weighted correlation network analysis")
+ (description
+ "This package provides functions necessary to perform Weighted
+Correlation Network Analysis on high-dimensional data. It includes functions
+for rudimentary data cleaning, construction and summarization of correlation
+networks, module identification and functions for relating both variables and
+modules to sample traits. It also includes a number of utility functions for
+data manipulation and visualization.")
+ (license license:gpl2+)))
+
+(define-public r-rgraphviz
+ (package
+ (name "r-rgraphviz")
+ (version "2.32.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rgraphviz" version))
+ (sha256
+ (base32
+ "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
+ (properties `((upstream-name . "Rgraphviz")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-reproducible
+ (lambda _
+ ;; The replacement value is taken from src/graphviz/builddate.h
+ (substitute* "src/graphviz/configure"
+ (("VERSION_DATE=.*")
+ "VERSION_DATE=20200427.2341\n"))
+ #t)))))
+ ;; FIXME: Rgraphviz bundles the sources of an older variant of
+ ;; graphviz. It does not build with the latest version of graphviz, so
+ ;; we do not add graphviz to the inputs.
+ (inputs `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-graph" ,r-graph)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "https://bioconductor.org/packages/Rgraphviz")
+ (synopsis "Plotting capabilities for R graph objects")
+ (description
+ "This package interfaces R with the graphviz library for plotting R graph
+objects from the @code{graph} package.")
+ (license license:epl1.0)))
+
+(define-public r-fithic
+ (package
+ (name "r-fithic")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "FitHiC" version))
+ (sha256
+ (base32
+ "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
+ (properties `((upstream-name . "FitHiC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-fdrtool" ,r-fdrtool)
+ ("r-rcpp" ,r-rcpp)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/FitHiC")
+ (synopsis "Confidence estimation for intra-chromosomal contact maps")
+ (description
+ "Fit-Hi-C is a tool for assigning statistical confidence estimates to
+intra-chromosomal contact maps produced by genome-wide genome architecture
+assays such as Hi-C.")
+ (license license:gpl2+)))
+
+(define-public r-hitc
+ (package
+ (name "r-hitc")
+ (version "1.32.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HiTC" version))
+ (sha256
+ (base32
+ "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
+ (properties `((upstream-name . "HiTC")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rtracklayer" ,r-rtracklayer)))
+ (home-page "https://bioconductor.org/packages/HiTC")
+ (synopsis "High throughput chromosome conformation capture analysis")
+ (description
+ "The HiTC package was developed to explore high-throughput \"C\" data
+such as 5C or Hi-C. Dedicated R classes as well as standard methods for
+quality controls, normalization, visualization, and further analysis are also
+provided.")
+ (license license:artistic2.0)))
+
+(define-public r-hdf5array
+ (package
+ (name "r-hdf5array")
+ (version "1.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "HDF5Array" version))
+ (sha256
+ (base32
+ "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
+ (properties `((upstream-name . "HDF5Array")))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rhdf5lib" ,r-rhdf5lib)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/HDF5Array")
+ (synopsis "HDF5 back end for DelayedArray objects")
+ (description "This package provides an array-like container for convenient
+access and manipulation of HDF5 datasets. It supports delayed operations and
+block processing.")
+ (license license:artistic2.0)))
+
+(define-public r-rhdf5lib
+ (package
+ (name "r-rhdf5lib")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Rhdf5lib" version))
+ (sha256
+ (base32
+ "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled binaries
+ (delete-file-recursively "src/wininclude/")
+ (delete-file-recursively "src/winlib-4.9.3/")
+ (delete-file-recursively "src/winlib-8.3.0/")
+ (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
+ #t))))
+ (properties `((upstream-name . "Rhdf5lib")))
+ (build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'do-not-use-bundled-hdf5
+ (lambda* (#:key inputs #:allow-other-keys)
+ (for-each delete-file '("configure" "configure.ac"))
+ ;; Do not make other packages link with the proprietary libsz.
+ (substitute* "R/zzz.R"
+ ((" \"%s/libsz.a\"") ""))
+ (with-directory-excursion "src"
+ (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
+ (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
+ "hdf5")
+ ;; Remove timestamp and host system information to make
+ ;; the build reproducible.
+ (substitute* "hdf5/src/libhdf5.settings.in"
+ (("Configured on: @CONFIG_DATE@")
+ "Configured on: Guix")
+ (("Uname information:.*")
+ "Uname information: Linux\n")
+ ;; Remove unnecessary store reference.
+ (("C Compiler:.*")
+ "C Compiler: GCC\n"))
+ (rename-file "Makevars.in" "Makevars")
+ (substitute* "Makevars"
+ (("@ZLIB_LIB@") "-lz")
+ (("@ZLIB_INCLUDE@") "")
+ (("HDF5_CXX_LIB=.*")
+ (string-append "HDF5_CXX_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
+ (("HDF5_LIB=.*")
+ (string-append "HDF5_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
+ (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
+ (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
+ (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
+ (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
+ (("HDF5_HL_LIB=.*")
+ (string-append "HDF5_HL_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
+ (("HDF5_HL_CXX_LIB=.*")
+ (string-append "HDF5_HL_CXX_LIB="
+ (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
+ ;; szip is non-free software
+ (("cp \"\\$\\{SZIP_LIB\\}.*") "")
+ (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (propagated-inputs
+ `(("hdf5" ,hdf5-1.10)))
+ (native-inputs
+ `(("hdf5-source" ,(package-source hdf5-1.10))
+ ("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/Rhdf5lib")
+ (synopsis "HDF5 library as an R package")
+ (description "This package provides C and C++ HDF5 libraries for use in R
+packages.")
+ (license license:artistic2.0)))
+
+(define-public r-beachmat
+ (package
+ (name "r-beachmat")
+ (version "2.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "beachmat" version))
+ (sha256
+ (base32
+ "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-matrix" ,r-matrix)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/beachmat")
+ (synopsis "Compiling Bioconductor to handle each matrix type")
+ (description "This package provides a consistent C++ class interface for a
+variety of commonly used matrix types, including sparse and HDF5-backed
+matrices.")
+ (license license:gpl3)))
+
+(define-public r-singlecellexperiment
+ (package
+ (name "r-singlecellexperiment")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "SingleCellExperiment" version))
+ (sha256
+ (base32
+ "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
+ (properties
+ `((upstream-name . "SingleCellExperiment")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/SingleCellExperiment")
+ (synopsis "S4 classes for single cell data")
+ (description "This package defines an S4 class for storing data from
+single-cell experiments. This includes specialized methods to store and
+retrieve spike-in information, dimensionality reduction coordinates and size
+factors for each cell, along with the usual metadata for genes and
+libraries.")
+ (license license:gpl3)))
+
+(define-public r-scater
+ (package
+ (name "r-scater")
+ (version "1.16.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scater" version))
+ (sha256
+ (base32
+ "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-ggbeeswarm" ,r-ggbeeswarm)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rlang" ,r-rlang)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-viridis" ,r-viridis)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/davismcc/scater")
+ (synopsis "Single-cell analysis toolkit for gene expression data in R")
+ (description "This package provides a collection of tools for doing
+various analyses of single-cell RNA-seq gene expression data, with a focus on
+quality control.")
+ (license license:gpl2+)))
+
+(define-public r-scran
+ (package
+ (name "r-scran")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scran" version))
+ (sha256
+ (base32
+ "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-beachmat" ,r-beachmat)
+ ("r-bh" ,r-bh)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocneighbors" ,r-biocneighbors)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-biocsingular" ,r-biocsingular)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-delayedmatrixstats" ,r-delayedmatrixstats)
+ ("r-dqrng" ,r-dqrng)
+ ("r-edger" ,r-edger)
+ ("r-igraph" ,r-igraph)
+ ("r-iranges" ,r-iranges)
+ ("r-limma" ,r-limma)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scater" ,r-scater)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-statmod" ,r-statmod)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://bioconductor.org/packages/scran")
+ (synopsis "Methods for single-cell RNA-Seq data analysis")
+ (description "This package implements a variety of low-level analyses of
+single-cell RNA-seq data. Methods are provided for normalization of
+cell-specific biases, assignment of cell cycle phase, and detection of highly
+variable and significantly correlated genes.")
+ (license license:gpl3)))
+
+(define-public r-delayedmatrixstats
+ (package
+ (name "r-delayedmatrixstats")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DelayedMatrixStats" version))
+ (sha256
+ (base32
+ "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
+ (properties
+ `((upstream-name . "DelayedMatrixStats")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-delayedarray" ,r-delayedarray)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-s4vectors" ,r-s4vectors)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
+ (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
+ (description
+ "This package provides a port of the @code{matrixStats} API for use with
+@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
+contains high-performing functions operating on rows and columns of
+@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
+@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
+are optimized per data type and for subsetted calculations such that both
+memory usage and processing time is minimized.")
+ (license license:expat)))
HCoop / jackhill / guix / guix.git / blobdiff