recipe bioconductor-excluderanges

Genomic coordinates of problematic genomic regions

Homepage:

https://bioconductor.org/packages/3.18/data/annotation/html/excluderanges.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-excluderanges/meta.yaml

Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC 'gap' table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.

package bioconductor-excluderanges

(downloads) docker_bioconductor-excluderanges

versions:

0.99.8-1,  0.99.8-0,  0.99.6-2,  0.99.6-1,  0.99.6-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

requirements:

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-excluderanges

and update with::

   mamba update bioconductor-excluderanges

To create a new environment, run:

mamba create --name myenvname bioconductor-excluderanges

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-excluderanges:<tag>

(see `bioconductor-excluderanges/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-excluderanges/README.html)