recipe bioconductor-bbcanalyzer

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-bbcanalyzer/meta.yaml

Links:

biotools: bbcanalyzer, doi: 10.1186/s12859-017-1549-4

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

package bioconductor-bbcanalyzer

versions:

1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0, 

1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

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-bbcanalyzer

and update with::

   mamba update bioconductor-bbcanalyzer

To create a new environment, run:

mamba create --name myenvname bioconductor-bbcanalyzer

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-bbcanalyzer:<tag>

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

Download stats

Link to this page

Render an 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-bbcanalyzer/README.html)