Package Recipe 'bioconductor-easyrnaseq'

recipe bioconductor-easyrnaseq

Count summarization and normalization for RNA-Seq data

Homepage: https://bioconductor.org/packages/3.11/bioc/html/easyRNASeq.html
License: Artistic-2.0
Recipe: /bioconductor-easyrnaseq/meta.yaml
Links: biotools: easyrnaseq

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.

package bioconductor-easyrnaseq¶

Versions

2.24.1-0, 2.22.0-0, 2.20.0-1, 2.18.2-0, 2.16.0-0, 2.14.0-0

Depends

bioconductor-biobase >=2.48.0,<2.49.0
bioconductor-biocfilecache >=1.12.0,<1.13.0
bioconductor-biocgenerics >=0.34.0,<0.35.0
bioconductor-biocparallel >=1.22.0,<1.23.0
bioconductor-biomart >=2.44.0,<2.45.0
bioconductor-biostrings >=2.56.0,<2.57.0
bioconductor-deseq >=1.39.0,<1.40.0
bioconductor-edger >=3.30.0,<3.31.0
bioconductor-genomeinfodb >=1.24.0,<1.25.0
bioconductor-genomeintervals >=1.43.0,<1.44.0
bioconductor-genomicalignments >=1.24.0,<1.25.0
bioconductor-genomicranges >=1.40.0,<1.41.0
bioconductor-iranges >=2.22.0,<2.23.0
bioconductor-rsamtools >=2.4.0,<2.5.0
bioconductor-s4vectors >=0.26.0,<0.27.0
bioconductor-shortread >=1.46.0,<1.47.0
bioconductor-summarizedexperiment >=1.18.0,<1.19.0
r-base >=4.0,<4.1.0a0
r-locfit
r-lsd >=4.0
r-rappdirs >=0.3.1

Required By

bioconductor-msgbsr

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-easyrnaseq

and update with:

conda update bioconductor-easyrnaseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-easyrnaseq:<tag>

(see bioconductor-easyrnaseq/tags for valid values for <tag>)

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-easyrnaseq/README.html)