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Source: pigx-rnaseq
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
autoconf-archive,
fastp,
fastqc <!nocheck>,
hisat2 <!nocheck>,
libjs-jquery-datatables <!nocheck>,
libjs-jquery-tablesorter <!nocheck>,
megadepth,
multiqc,
python3-all,
python3-deeptools,
python3-htseq,
r-bioc-deseq2 <!nocheck>,
r-bioc-rtracklayer <!nocheck>,
r-bioc-summarizedexperiment <!nocheck>,
r-bioc-tximport <!nocheck>,
r-cran-corrplot <!nocheck>,
r-cran-crosstalk <!nocheck>,
r-cran-data.table <!nocheck>,
r-cran-dt <!nocheck>,
r-cran-ggplot2 <!nocheck>,
r-cran-ggrepel <!nocheck>,
r-cran-gprofiler2 <!nocheck>,
r-cran-ggpubr <!nocheck>,
r-cran-locfit <!nocheck>,
r-cran-pheatmap <!nocheck>,
r-cran-plotly <!nocheck>,
r-cran-reshape2 <!nocheck>,
r-cran-rjson <!nocheck>,
r-cran-rlang <!nocheck>,
r-cran-rmarkdown <!nocheck>,
r-cran-scales <!nocheck>,
salmon <!nocheck>,
samtools <!nocheck>,
snakemake <!nocheck>,
trim-galore <!nocheck>
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/pigx-rnaseq
Vcs-Git: https://salsa.debian.org/med-team/pigx-rnaseq.git
Homepage: https://github.com/BIMSBbioinfo/pigx_rnaseq
Rules-Requires-Root: no
Package: pigx-rnaseq
Architecture: all
Depends: ${misc:Depends},
fastp,
fastqc,
hisat2 | rna-star,
libjs-jquery-datatables,
libjs-jquery-tablesorter,
megadepth,
multiqc,
python3:any,
python3-deeptools,
python3-htseq,
r-bioc-deseq2,
r-bioc-rtracklayer,
r-bioc-summarizedexperiment,
r-bioc-tximport,
r-cran-corrplot,
r-cran-crosstalk,
r-cran-data.table,
r-cran-dt,
r-cran-ggplot2,
r-cran-ggpubr,
r-cran-ggrepel,
r-cran-gprofiler2,
r-cran-pheatmap,
r-cran-plotly,
r-cran-reshape2,
r-cran-rjson,
r-cran-rlang,
r-cran-rmarkdown,
r-cran-scales,
salmon,
samtools,
snakemake,
trim-galore
Recommends: hisat2, rna-star
Description: pipeline for checkpointed and distributed RNA-seq analyses
This package provides a automated workflow for the automated analysis of
RNA-seq experiments. A series of well-accecpted tools are connected in
Python scripts and controlled via snakemake. This supports the parallel
execution of these workflows and provides checkpointing, such that
interrupted workflows can take up their work again.
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