recipe bioconductor-recount

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/recount.html

License

Artistic-2.0

Recipe

/bioconductor-recount/meta.yaml

package bioconductor-recount

Versions

1.8.1-0, 1.6.3-0, 1.4.5-0, 1.4.0-0

Depends

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-derfinder >=1.16.0,<1.17.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-geoquery >=2.50.0,<2.51.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• r-base >=3.5.1,<3.5.2.0a0

• r-downloader

• r-rcurl

• r-rentrez

Required By

• bioconductor-psichomics

Installation

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

conda install bioconductor-recount

and update with:

conda update bioconductor-recount

or use the docker container:

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

(see bioconductor-recount/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-recount/README.html)