recipe bioconductor-vulcan

VirtUaL ChIP-Seq data Analysis using Networks

Homepage

https://bioconductor.org/packages/3.11/bioc/html/vulcan.html

License

LGPL-3

Recipe

/bioconductor-vulcan/meta.yaml

Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.

package bioconductor-vulcan

Versions

1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-chippeakanno >=3.22.0,<3.23.0

• bioconductor-csaw >=1.22.0,<1.23.0

• bioconductor-deseq >=1.39.0,<1.40.0

• bioconductor-diffbind >=2.16.0,<2.17.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-viper >=1.22.0,<1.23.0

• r-base >=4.0,<4.1.0a0

• r-catools

• r-gplots

• r-locfit

• r-wordcloud

• r-zoo

Required By

Installation

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

conda install bioconductor-vulcan

and update with:

conda update bioconductor-vulcan

or use the docker container:

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

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

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-vulcan/README.html)