recipe bioconductor-gdnainrnaseqdata

RNA-seq data with different levels of gDNA contamination

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/gDNAinRNAseqData.html

License:

Artistic-2.0

Recipe:

/bioconductor-gdnainrnaseqdata/meta.yaml

Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.

package bioconductor-gdnainrnaseqdata

(downloads) docker_bioconductor-gdnainrnaseqdata

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-rcurl:

depends r-xml:

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-gdnainrnaseqdata

and update with::

   mamba update bioconductor-gdnainrnaseqdata

To create a new environment, run:

mamba create --name myenvname bioconductor-gdnainrnaseqdata

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-gdnainrnaseqdata:<tag>

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

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Link to this page

Render an install-with-bioconda 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-gdnainrnaseqdata/README.html)