recipe bioconductor-recount3

Explore and download data from the recount3 project

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/recount3.html

License:

Artistic-2.0

Recipe:

/bioconductor-recount3/meta.yaml

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

package bioconductor-recount3

versions:

1.12.0-0,  1.10.2-0,  1.8.0-0,  1.4.0-0,  1.2.1-0,  1.0.7-0,  1.0.0-1

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-httr:

depends r-matrix:

depends r-r.utils:

depends r-sessioninfo:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-recount3

and update with::

   mamba update bioconductor-recount3

To create a new environment, run:

mamba create --name myenvname bioconductor-recount3

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-recount3:<tag>

(see `bioconductor-recount3/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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