bioconductor-baalchip

downloads

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.

Home http://bioconductor.org/packages/3.7/bioc/html/BaalChIP.html
Versions 1.6.0, 1.4.0
License Artistic-2.0
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-baalchip
Links biotools: baalchip, doi: 10.1186/s13059-017-1165-7

Installation

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

conda install bioconductor-baalchip

and update with:

conda update bioconductor-baalchip

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-baalchip.