recipe bioconductor-bamsignals

Extract read count signals from bam files

Homepage:

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

License:

GPL-2.0-only

Recipe:

/bioconductor-bamsignals/meta.yaml

Links:

biotools: bamsignals, doi: 10.1038/nmeth.3252

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

package bioconductor-bamsignals

versions:

1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.24.0-0, 

1.34.0-1,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.30.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0,  1.12.1-0,  1.10.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0a0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0

depends bioconductor-zlibbioc:

>=1.48.0,<1.49.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-rcpp:

>=0.10.6

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-bamsignals

and update with::

   mamba update bioconductor-bamsignals

To create a new environment, run:

mamba create --name myenvname bioconductor-bamsignals

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-bamsignals:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-bamsignals/README.html)