- recipe bioconductor-recount
Explore and download data from the recount project
- Homepage:
https://bioconductor.org/packages/3.14/bioc/html/recount.html
- License:
Artistic-2.0
- Recipe:
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.
- package bioconductor-recount¶
-
- Versions:
1.20.0-0
,1.18.0-0
,1.16.1-0
,1.16.0-0
,1.14.0-0
,1.12.0-0
,1.10.8-0
,1.8.1-0
,1.6.3-0
,1.20.0-0
,1.18.0-0
,1.16.1-0
,1.16.0-0
,1.14.0-0
,1.12.0-0
,1.10.8-0
,1.8.1-0
,1.6.3-0
,1.4.5-0
,1.4.0-0
- Depends:
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-derfinder
>=1.28.0,<1.29.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-geoquery
>=2.62.0,<2.63.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
r-base
>=4.1,<4.2.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-recount/README.html)