recipe bioconductor-easyrnaseq

Count summarization and normalization for RNA-Seq data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/easyRNASeq.html

License

Artistic-2.0

Recipe

/bioconductor-easyrnaseq/meta.yaml

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

2.28.0-0,  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 >=2.52.0,<2.53.0

• bioconductor-biocfilecache >=2.0.0,<2.1.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biomart >=2.48.0,<2.49.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-edger >=3.34.0,<3.35.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomeintervals >=1.48.0,<1.49.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-shortread >=1.50.0,<1.51.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• r-base >=4.1,<4.2.0a0

• r-locfit

• r-lsd >=4.1-0

• 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

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