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/3.9/bioc/html/easyRNASeq.html

License

Artistic-2.0

Recipe

/bioconductor-easyrnaseq/meta.yaml

Links

biotools: easyrnaseq

package bioconductor-easyrnaseq

(downloads) docker_bioconductor-easyrnaseq

Versions

2.18.2-0, 2.16.0-0, 2.14.0-0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-biomart

>=2.38.0,<2.39.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-deseq

>=1.34.0,<1.35.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomeintervals

>=1.38.0,<1.39.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-shortread

>=1.40.0,<1.41.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-locfit

Depends r-lsd

>=3.0

Requirements

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>)