374 lines
14 KiB
Scheme
374 lines
14 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages bioconductor)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix build-system r)
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#:use-module (gnu packages)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages bioinformatics))
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(define-public r-bsgenome-dmelanogaster-ucsc-dm6
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(package
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(name "r-bsgenome-dmelanogaster-ucsc-dm6")
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(version "1.4.1")
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(source (origin
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(method url-fetch)
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;; We cannot use bioconductor-uri here because this tarball is
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;; located under "data/annotation/" instead of "bioc/".
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(uri (string-append "https://www.bioconductor.org/packages/"
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"release/data/annotation/src/contrib/"
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"BSgenome.Dmelanogaster.UCSC.dm6_"
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version ".tar.gz"))
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(sha256
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(base32
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"1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
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(properties
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`((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
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(build-system r-build-system)
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;; As this package provides little more than a very large data file it
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;; doesn't make sense to build substitutes.
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(arguments `(#:substitutable? #f))
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(propagated-inputs
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`(("r-bsgenome" ,r-bsgenome)))
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(home-page
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"https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
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(synopsis "Full genome sequences for Fly")
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(description
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"This package provides full genome sequences for Drosophila
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melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
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objects.")
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(license license:artistic2.0)))
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(define-public r-hpar
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(package
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(name "r-hpar")
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(version "1.22.2")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "hpar" version))
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(sha256
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(base32
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"1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
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(build-system r-build-system)
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(home-page "https://bioconductor.org/packages/hpar/")
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(synopsis "Human Protein Atlas in R")
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(description "This package provides a simple interface to and data from
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the Human Protein Atlas project.")
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(license license:artistic2.0)))
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(define-public r-regioner
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(package
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(name "r-regioner")
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(version "1.12.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "regioneR" version))
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(sha256
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(base32
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"09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
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(properties `((upstream-name . "regioneR")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-memoise" ,r-memoise)
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("r-genomicranges" ,r-genomicranges)
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("r-bsgenome" ,r-bsgenome)
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("r-rtracklayer" ,r-rtracklayer)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-iranges" ,r-iranges)
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("r-s4vectors" ,r-s4vectors)))
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(home-page "https://bioconductor.org/packages/regioneR/")
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(synopsis "Association analysis of genomic regions")
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(description "This package offers a statistical framework based on
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customizable permutation tests to assess the association between genomic
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region sets and other genomic features.")
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(license license:artistic2.0)))
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(define-public r-diffbind
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(package
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(name "r-diffbind")
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(version "2.8.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "DiffBind" version))
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(sha256
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(base32
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"1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
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(properties `((upstream-name . "DiffBind")))
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(build-system r-build-system)
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(inputs
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`(("zlib" ,zlib)))
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(propagated-inputs
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`(("r-amap" ,r-amap)
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("r-biocparallel" ,r-biocparallel)
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("r-deseq2" ,r-deseq2)
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("r-dplyr" ,r-dplyr)
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("r-edger" ,r-edger)
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("r-genomicalignments" ,r-genomicalignments)
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("r-genomicranges" ,r-genomicranges)
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("r-ggplot2" ,r-ggplot2)
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("r-ggrepel" ,r-ggrepel)
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("r-gplots" ,r-gplots)
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("r-iranges" ,r-iranges)
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("r-lattice" ,r-lattice)
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("r-limma" ,r-limma)
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("r-locfit" ,r-locfit)
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("r-rcolorbrewer" , r-rcolorbrewer)
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("r-rcpp" ,r-rcpp)
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("r-rsamtools" ,r-rsamtools)
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("r-s4vectors" ,r-s4vectors)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-systempiper" ,r-systempiper)
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("r-zlibbioc" ,r-zlibbioc)))
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(home-page "http://bioconductor.org/packages/DiffBind")
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(synopsis "Differential binding analysis of ChIP-Seq peak data")
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(description
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"This package computes differentially bound sites from multiple
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ChIP-seq experiments using affinity (quantitative) data. Also enables
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occupancy (overlap) analysis and plotting functions.")
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(license license:artistic2.0)))
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(define-public r-ripseeker
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(package
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(name "r-ripseeker")
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(version "1.20.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "RIPSeeker" version))
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(sha256
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(base32
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"0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
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(properties `((upstream-name . "RIPSeeker")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-s4vectors" ,r-s4vectors)
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("r-iranges" ,r-iranges)
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("r-genomicranges" ,r-genomicranges)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-rsamtools" ,r-rsamtools)
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("r-genomicalignments" ,r-genomicalignments)
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("r-rtracklayer" ,r-rtracklayer)))
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(home-page "http://bioconductor.org/packages/RIPSeeker")
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(synopsis
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"Identifying protein-associated transcripts from RIP-seq experiments")
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(description
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"This package infers and discriminates RIP peaks from RIP-seq alignments
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using two-state HMM with negative binomial emission probability. While
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RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
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a suite of bioinformatics tools integrated within this self-contained software
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package comprehensively addressing issues ranging from post-alignments
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processing to visualization and annotation.")
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(license license:gpl2)))
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(define-public r-multtest
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(package
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(name "r-multtest")
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(version "2.36.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "multtest" version))
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(sha256
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(base32
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"11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-survival" ,r-survival)
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("r-biocgenerics" ,r-biocgenerics)
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("r-biobase" ,r-biobase)
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("r-mass" ,r-mass)))
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(home-page "http://bioconductor.org/packages/multtest")
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(synopsis "Resampling-based multiple hypothesis testing")
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(description
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"This package can do non-parametric bootstrap and permutation
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resampling-based multiple testing procedures (including empirical Bayes
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methods) for controlling the family-wise error rate (FWER), generalized
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family-wise error rate (gFWER), tail probability of the proportion of
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false positives (TPPFP), and false discovery rate (FDR). Several choices
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of bootstrap-based null distribution are implemented (centered, centered
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and scaled, quantile-transformed). Single-step and step-wise methods are
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available. Tests based on a variety of T- and F-statistics (including
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T-statistics based on regression parameters from linear and survival models
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as well as those based on correlation parameters) are included. When probing
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hypotheses with T-statistics, users may also select a potentially faster null
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distribution which is multivariate normal with mean zero and variance
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covariance matrix derived from the vector influence function. Results are
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reported in terms of adjusted P-values, confidence regions and test statistic
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cutoffs. The procedures are directly applicable to identifying differentially
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expressed genes in DNA microarray experiments.")
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(license license:lgpl3)))
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(define-public r-chippeakanno
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(package
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(name "r-chippeakanno")
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(version "3.14.0")
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(source
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(origin
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(method url-fetch)
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(uri (bioconductor-uri "ChIPpeakAnno" version))
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(sha256
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(base32
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"1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
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(properties `((upstream-name . "ChIPpeakAnno")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-delayedarray" ,r-delayedarray)
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("r-go-db" ,r-go-db)
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("r-biomart" ,r-biomart)
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("r-bsgenome" ,r-bsgenome)
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("r-genomicfeatures" ,r-genomicfeatures)
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("r-genomicranges" ,r-genomicranges)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-iranges" ,r-iranges)
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("r-matrixstats" ,r-matrixstats)
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("r-annotationdbi" ,r-annotationdbi)
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("r-limma" ,r-limma)
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("r-multtest" ,r-multtest)
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("r-rbgl" ,r-rbgl)
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("r-graph" ,r-graph)
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("r-biocinstaller" ,r-biocinstaller)
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("r-regioner" ,r-regioner)
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("r-dbi" ,r-dbi)
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("r-ensembldb" ,r-ensembldb)
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("r-biobase" ,r-biobase)
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("r-s4vectors" ,r-s4vectors)
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("r-seqinr" ,r-seqinr)
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("r-idr" ,r-idr)
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("r-genomicalignments" ,r-genomicalignments)
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("r-summarizedexperiment" ,r-summarizedexperiment)
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("r-rsamtools" ,r-rsamtools)
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("r-venndiagram" ,r-venndiagram)))
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(home-page "http://bioconductor.org/packages/ChIPpeakAnno")
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(synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
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(description
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"The package includes functions to retrieve the sequences around the peak,
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obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
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custom features such as most conserved elements and other transcription factor
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binding sites supplied by users. Starting 2.0.5, new functions have been added
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for finding the peaks with bi-directional promoters with summary statistics
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(peaksNearBDP), for summarizing the occurrence of motifs in peaks
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(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
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enrichedGO (addGeneIDs).")
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(license license:gpl2+)))
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(define-public r-marray
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(package
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(name "r-marray")
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(version "1.58.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "marray" version))
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(sha256
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(base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-limma" ,r-limma)))
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(home-page "http://bioconductor.org/packages/marray")
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(synopsis "Exploratory analysis for two-color spotted microarray data")
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(description "This package contains class definitions for two-color spotted
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microarray data. It also includes fuctions for data input, diagnostic plots,
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normalization and quality checking.")
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(license license:lgpl2.0+)))
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(define-public r-cghbase
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(package
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(name "r-cghbase")
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(version "1.40.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "CGHbase" version))
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(sha256
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(base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
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(properties `((upstream-name . "CGHbase")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biobase" ,r-biobase)
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("r-marray" ,r-marray)))
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(home-page "http://bioconductor.org/packages/CGHbase")
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(synopsis "Base functions and classes for arrayCGH data analysis")
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(description "This package contains functions and classes that are needed by
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the @code{arrayCGH} packages.")
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(license license:gpl2+)))
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(define-public r-cghcall
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(package
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(name "r-cghcall")
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(version "2.42.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "CGHcall" version))
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(sha256
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(base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
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(properties `((upstream-name . "CGHcall")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biobase" ,r-biobase)
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("r-cghbase" ,r-cghbase)
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("r-impute" ,r-impute)
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("r-dnacopy" ,r-dnacopy)
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("r-snowfall" ,r-snowfall)))
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(home-page "http://bioconductor.org/packages/CGHcall")
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(synopsis "Base functions and classes for arrayCGH data analysis")
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(description "This package contains functions and classes that are needed by
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@code{arrayCGH} packages.")
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(license license:gpl2+)))
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(define-public r-qdnaseq
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(package
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(name "r-qdnaseq")
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(version "1.16.0")
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(source (origin
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(method url-fetch)
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(uri (bioconductor-uri "QDNAseq" version))
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(sha256
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(base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
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(properties `((upstream-name . "QDNAseq")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biobase" ,r-biobase)
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("r-biocparallel" ,r-biocparallel)
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("r-cghbase" ,r-cghbase)
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("r-cghcall" ,r-cghcall)
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("r-dnacopy" ,r-dnacopy)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-matrixstats" ,r-matrixstats)
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("r-r-utils" ,r-r-utils)
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("r-rsamtools" ,r-rsamtools)))
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(home-page "http://bioconductor.org/packages/QDNAseq")
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(synopsis "Quantitative DNA sequencing for chromosomal aberrations")
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(description "The genome is divided into non-overlapping fixed-sized bins,
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number of sequence reads in each counted, adjusted with a simultaneous
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two-dimensional loess correction for sequence mappability and GC content, and
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filtered to remove spurious regions in the genome. Downstream steps of
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segmentation and calling are also implemented via packages DNAcopy and CGHcall,
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respectively.")
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(license license:gpl2+)))
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