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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages bioconductor)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
#:use-module (gnu packages statistics)
#:use-module (gnu packages bioinformatics))
(define-public r-hpar
(package
(name "r-hpar")
(version "1.20.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "hpar" version))
(sha256
(base32
"0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
(build-system r-build-system)
(home-page "https://bioconductor.org/packages/hpar/")
(synopsis "Human Protein Atlas in R")
(description "This package provides a simple interface to and data from
the Human Protein Atlas project.")
(license license:artistic2.0)))
(define-public r-regioner
(package
(name "r-regioner")
(version "1.10.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
"1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
`(("r-memoise" ,r-memoise)
("r-genomicranges" ,r-genomicranges)
("r-bsgenome" ,r-bsgenome)
("r-rtracklayer" ,r-rtracklayer)
("r-genomeinfodb" ,r-genomeinfodb)
("r-iranges" ,r-iranges)))
(home-page "https://bioconductor.org/packages/regioneR/")
(synopsis "Association analysis of genomic regions")
(description "This package offers a statistical framework based on
customizable permutation tests to assess the association between genomic
region sets and other genomic features.")
(license license:artistic2.0)))
(define-public r-diffbind
(package
(name "r-diffbind")
(version "2.6.6")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
"1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(propagated-inputs
`(("r-amap" ,r-amap)
("r-biocparallel" ,r-biocparallel)
("r-deseq2" ,r-deseq2)
("r-dplyr" ,r-dplyr)
("r-edger" ,r-edger)
("r-genomicalignments" ,r-genomicalignments)
("r-ggrepel" ,r-ggrepel)
("r-gplots" ,r-gplots)
("r-iranges" ,r-iranges)
("r-lattice" ,r-lattice)
("r-limma" ,r-limma)
("r-locfit" ,r-locfit)
("r-rcolorbrewer" , r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-systempiper" ,r-systempiper)
("r-zlibbioc" ,r-zlibbioc)))
(home-page "http://bioconductor.org/packages/DiffBind")
(synopsis "Differential binding analysis of ChIP-Seq peak data")
(description
"This package computes differentially bound sites from multiple
ChIP-seq experiments using affinity (quantitative) data. Also enables
occupancy (overlap) analysis and plotting functions.")
(license license:artistic2.0)))
(define-public r-ripseeker
(package
(name "r-ripseeker")
(version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RIPSeeker" version))
(sha256
(base32
"0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
(properties `((upstream-name . "RIPSeeker")))
(build-system r-build-system)
(propagated-inputs
`(("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
("r-genomicranges" ,r-genomicranges)
("r-summarizedexperiment" ,r-summarizedexperiment)
("r-rsamtools" ,r-rsamtools)
("r-genomicalignments" ,r-genomicalignments)
("r-rtracklayer" ,r-rtracklayer)))
(home-page "http://bioconductor.org/packages/RIPSeeker")
(synopsis
"Identifying protein-associated transcripts from RIP-seq experiments")
(description
"This package infers and discriminates RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission probability. While
RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
a suite of bioinformatics tools integrated within this self-contained software
package comprehensively addressing issues ranging from post-alignments
processing to visualization and annotation.")
(license license:gpl2)))
(define-public r-multtest
(package
(name "r-multtest")
(version "2.34.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "multtest" version))
(sha256
(base32
"0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-survival" ,r-survival)
("r-biocgenerics" ,r-biocgenerics)
("r-biobase" ,r-biobase)
("r-mass" ,r-mass)))
(home-page "http://bioconductor.org/packages/multtest")
(synopsis "Resampling-based multiple hypothesis testing")
(description
"This package can do non-parametric bootstrap and permutation
resampling-based multiple testing procedures (including empirical Bayes
methods) for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the proportion of
false positives (TPPFP), and false discovery rate (FDR). Several choices
of bootstrap-based null distribution are implemented (centered, centered
and scaled, quantile-transformed). Single-step and step-wise methods are
available. Tests based on a variety of T- and F-statistics (including
T-statistics based on regression parameters from linear and survival models
as well as those based on correlation parameters) are included. When probing
hypotheses with T-statistics, users may also select a potentially faster null
distribution which is multivariate normal with mean zero and variance
covariance matrix derived from the vector influence function. Results are
reported in terms of adjusted P-values, confidence regions and test statistic
cutoffs. The procedures are directly applicable to identifying differentially
expressed genes in DNA microarray experiments.")
(license license:lgpl3)))
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