recipe bioconductor-baalchip

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/BaalChIP.html

License

Artistic-2.0

Recipe

/bioconductor-baalchip/meta.yaml

Links

biotools: baalchip, doi: 10.1186/s13059-017-1165-7

package bioconductor-baalchip

(downloads) docker_bioconductor-baalchip

Versions

1.8.0-0, 1.6.0-0, 1.4.0-0

Depends
Required By

Installation

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

conda install bioconductor-baalchip

and update with:

conda update bioconductor-baalchip

or use the docker container:

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

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