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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
_pkgname=GRaNIE
_pkgver=1.6.1
pkgname=r-${_pkgname,,}
pkgver=${_pkgver//-/.}
pkgrel=4
pkgdesc="Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data"
arch=(any)
url="https://bioconductor.org/packages/$_pkgname"
license=('Artistic-2.0')
depends=(
r-annotationhub
r-biomart
r-biostrings
r-checkmate
r-circlize
r-colorspace
r-complexheatmap
r-data.table
r-deseq2
r-dplyr
r-ensembldb
r-forcats
r-futile.logger
r-genomeinfodb
r-genomicranges
r-ggplot2
r-gridextra
r-igraph
r-limma
r-magrittr
r-matrixstats
r-patchwork
r-progress
r-rcolorbrewer
r-readr
r-reshape2
r-rlang
r-s4vectors
r-scales
r-stringr
r-summarizedexperiment
r-tibble
r-tidyr
r-tidyselect
r-topgo
r-viridis
)
optdepends=(
r-biocfilecache
r-biocparallel
r-biocstyle
r-bsgenome.dmelanogaster.ucsc.dm6
r-bsgenome.hsapiens.ucsc.hg19
r-bsgenome.hsapiens.ucsc.hg38
r-bsgenome.mmulatta.ucsc.rhemac10
r-bsgenome.mmusculus.ucsc.mm10
r-bsgenome.mmusculus.ucsc.mm9
r-bsgenome.rnorvegicus.ucsc.rn6
r-bsgenome.rnorvegicus.ucsc.rn7
r-chipseeker
r-clusterprofiler
r-csaw
r-dose
r-edaseq
r-ihw
r-jaspar2022
r-knitr
r-ldlinkr
r-motifmatchr
r-org.dm.eg.db
r-org.hs.eg.db
r-org.mm.eg.db
r-org.mmu.eg.db
r-org.rn.eg.db
r-purrr
r-rbioapi
r-reactomepa
r-testthat
r-tfbstools
r-txdb.dmelanogaster.ucsc.dm6.ensgene
r-txdb.hsapiens.ucsc.hg19.knowngene
r-txdb.hsapiens.ucsc.hg38.knowngene
r-txdb.mmulatta.ucsc.rhemac10.refgene
r-txdb.mmusculus.ucsc.mm10.knowngene
r-txdb.mmusculus.ucsc.mm9.knowngene
r-txdb.rnorvegicus.ucsc.rn6.refgene
r-txdb.rnorvegicus.ucsc.rn7.refgene
r-variancepartition
r-wgcna
)
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
md5sums=('d9db703063398ccd263ce6b54def9266')
b2sums=('79192e9cb4153a1ebf23e76daa0c9629bcdf36545108587914bf02e624cdd00033ccc7ec998bcdef229a8a9ea7bab3bc7d9806329350f6712d684429016d08cb')
build() {
mkdir build
R CMD INSTALL -l build "$_pkgname"
}
package() {
install -d "$pkgdir/usr/lib/R/library"
cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
}
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