recipe bioconductor-badregionfinder

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-badregionfinder/meta.yaml

Links:

biotools: badregionfinder, doi: 10.1038/nmeth.3252

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

package bioconductor-badregionfinder

(downloads) docker_bioconductor-badregionfinder

versions:
1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0, 

1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

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-badregionfinder

and update with::

   mamba update bioconductor-badregionfinder

To create a new environment, run:

mamba create --name myenvname bioconductor-badregionfinder

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-badregionfinder:<tag>

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