;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
+;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
#:use-module (gnu packages tcl)
#:use-module (gnu packages tls)
#:use-module (gnu packages web)
+ #:use-module (gnu packages xml)
#:use-module (gnu packages xorg))
(define-public r-rticles
model.")
(license license:gpl2)))
+(define-public r-igraph
+ (package
+ (name "r-igraph")
+ (version "1.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "igraph" version))
+ (sha256
+ (base32
+ "126z1ygbmi3g7hk97snf22rnx680dyi30idssm5zacba5rdngp8c"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ `(("gmp" ,gmp)
+ ("glpk" ,glpk)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (propagated-inputs
+ `(("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-pkgconfig" ,r-pkgconfig)))
+ (home-page "https://igraph.org")
+ (synopsis "Network analysis and visualization")
+ (description
+ "This package provides routines for simple graphs and network analysis.
+It can handle large graphs very well and provides functions for generating
+random and regular graphs, graph visualization, centrality methods and much
+more.")
+ (license license:gpl2+)))
+
(define-public r-workflows
(package
(name "r-workflows")
covariate (usually group indicator) and the scores.")
;; Any version of the GPL
(license license:gpl2+)))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.46-2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/qtl_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
+ (build-system r-build-system)
+ (home-page "https://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics
+system. It is used to analyze experimental crosses for identifying
+genes contributing to variation in quantitative traits (so-called
+quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl estimates genetic maps, to
+identify genotyping errors, and to perform single-QTL and two-QTL,
+two-dimensional genome scans.")
+ (license license:gpl3)))
+
+(define-public r-qtl2
+ (package
+ (name "r-qtl2")
+ (version "0.22-11")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "qtl2" version))
+ (sha256
+ (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-data-table" ,r-data-table)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rsqlite" ,r-rsqlite)
+ ("r-yaml" ,r-yaml)))
+ (home-page "https://kbroman.org/qtl2/")
+ (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
+ (description
+ "This package provides a set of tools to perform @dfn{Quantitative Trait
+Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
+@code{R/qtl} package to better handle high-dimensional data and complex cross
+designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
+ (license license:gpl3)))
+
+(define-public r-seqminer
+ (package
+ (name "r-seqminer")
+ (version "8.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "seqminer" version))
+ (sha256
+ (base32
+ "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
+ (build-system r-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "http://seqminer.genomic.codes")
+ (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
+ (description
+ "This package provides tools to integrate nucleotide sequencing
+data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
+ ;; Any version of the GPL is acceptable
+ (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-maldiquant
+ (package
+ (name "r-maldiquant")
+ (version "1.19.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "MALDIquant" version))
+ (sha256
+ (base32
+ "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
+ (properties `((upstream-name . "MALDIquant")))
+ (build-system r-build-system)
+ (home-page "https://cran.r-project.org/web/packages/MALDIquant")
+ (synopsis "Quantitative analysis of mass spectrometry data")
+ (description
+ "This package provides a complete analysis pipeline for matrix-assisted
+laser desorption/ionization-time-of-flight (MALDI-TOF) and other
+two-dimensional mass spectrometry data. In addition to commonly used plotting
+and processing methods it includes distinctive features, namely baseline
+subtraction methods such as morphological filters (TopHat) or the
+statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
+alignment using warping functions, handling of replicated measurements as well
+as allowing spectra with different resolutions.")
+ (license license:gpl3+)))
+
+(define-public r-seurat
+ (package
+ (name "r-seurat")
+ (version "3.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "Seurat" version))
+ (sha256
+ (base32
+ "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
+ (properties `((upstream-name . "Seurat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-cluster" ,r-cluster)
+ ("r-cowplot" ,r-cowplot)
+ ("r-fitdistrplus" ,r-fitdistrplus)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggridges" ,r-ggridges)
+ ("r-httr" ,r-httr)
+ ("r-ica" ,r-ica)
+ ("r-igraph" ,r-igraph)
+ ("r-irlba" ,r-irlba)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-kernsmooth" ,r-kernsmooth)
+ ("r-leiden" ,r-leiden)
+ ("r-lmtest" ,r-lmtest)
+ ("r-mass" ,r-mass)
+ ("r-matrix" ,r-matrix)
+ ("r-miniui" ,r-miniui)
+ ("r-patchwork" ,r-patchwork)
+ ("r-pbapply" ,r-pbapply)
+ ("r-plotly" ,r-plotly)
+ ("r-png" ,r-png)
+ ("r-rann" ,r-rann)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-rcppprogress" ,r-rcppprogress)
+ ("r-reticulate" ,r-reticulate)
+ ("r-rlang" ,r-rlang)
+ ("r-rocr" ,r-rocr)
+ ("r-rsvd" ,r-rsvd)
+ ("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-sctransform" ,r-sctransform)
+ ("r-shiny" ,r-shiny)
+ ("r-spatstat" ,r-spatstat)
+ ("r-tibble" ,r-tibble)
+ ("r-uwot" ,r-uwot)))
+ (home-page "http://www.satijalab.org/seurat")
+ (synopsis "Seurat is an R toolkit for single cell genomics")
+ (description
+ "This package is an R package designed for QC, analysis, and
+exploration of single cell RNA-seq data. It easily enables widely-used
+analytical techniques, including the identification of highly variable genes,
+dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
+algorithms; density clustering, hierarchical clustering, k-means, and the
+discovery of differentially expressed genes and markers.")
+ (license license:gpl3)))
+
+(define-public r-phangorn
+ (package
+ (name "r-phangorn")
+ (version "2.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "phangorn" version))
+ (sha256
+ (base32
+ "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-fastmatch" ,r-fastmatch)
+ ("r-igraph" ,r-igraph)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-quadprog" ,r-quadprog)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://github.com/KlausVigo/phangorn")
+ (synopsis "Phylogenetic analysis in R")
+ (description
+ "Phangorn is a package for phylogenetic analysis in R. It supports
+estimation of phylogenetic trees and networks using Maximum Likelihood,
+Maximum Parsimony, distance methods and Hadamard conjugation.")
+ (license license:gpl2+)))
+
+(define-public r-diversitree
+ (package
+ (name "r-diversitree")
+ (version "0.9-13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "diversitree" version))
+ (sha256
+ (base32
+ "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
+ (build-system r-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
+ (propagated-inputs
+ `(("r-ape" ,r-ape)
+ ("r-desolve" ,r-desolve)
+ ("r-rcpp" ,r-rcpp)
+ ("r-subplex" ,r-subplex)))
+ (home-page "https://www.zoology.ubc.ca/prog/diversitree")
+ (synopsis "Comparative 'phylogenetic' analyses of diversification")
+ (description "This package contains a number of comparative \"phylogenetic\"
+methods, mostly focusing on analysing diversification and character evolution.
+Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
+and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
+Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
+include Markov models of discrete and continuous trait evolution and constant
+rate speciation and extinction.")
+ (license license:gpl2+)))
HCoop / jackhill / guix / guix.git / blobdiff