recipe bioconductor-bamsignals

Extract read count signals from bam files

Homepage

https://bioconductor.org/packages/3.14/bioc/html/bamsignals.html

License

GPL-2

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

1.26.0-1,  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, 

1.26.0-1,  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 >=0.40.0,<0.41.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rhtslib >=1.26.0,<1.27.0

• bioconductor-zlibbioc >=1.40.0,<1.41.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• r-base >=4.1,<4.2.0a0

• r-rcpp >=0.10.6

Required By

• epicseg

• bioconductor-karyoploter

• bioconductor-normr

• bioconductor-chromstar

• bioconductor-segmenter

• bioconductor-epigrahmm

• bioconductor-aneufinder

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-bamsignals

and update with:

conda update bioconductor-bamsignals

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-bamsignals:<tag>

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

Download stats

Link to this page

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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)