recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/easyRNASeq.html

License

Artistic-2.0

Recipe

/bioconductor-easyrnaseq/meta.yaml

Links

biotools: easyrnaseq

package bioconductor-easyrnaseq

Versions

2.18.2-0, 2.16.0-0, 2.14.0-0

Depends

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-biomart >=2.38.0,<2.39.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-deseq >=1.34.0,<1.35.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomeintervals >=1.38.0,<1.39.0

• bioconductor-genomicalignments >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-shortread >=1.40.0,<1.41.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• r-base >=3.5.1,<3.5.2.0a0

• r-locfit

• r-lsd >=3.0

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)