recipe bioconductor-baalchip

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/BaalChIP.html

License:

Artistic-2.0

Recipe:

/bioconductor-baalchip/meta.yaml

Links:

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

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.

package bioconductor-baalchip

Versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0, 

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0

Depends:

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• r-base >=4.2,<4.3.0a0

• r-coda

• r-doby

• r-doparallel

• r-foreach

• r-ggplot2

• r-reshape2

• r-scales

Required By:

Installation

With an activated Bioconda channel (see 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>)

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-baalchip/README.html)