recipe bioconductor-vulcan

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.

Homepage

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

License

LGPL-3

Recipe

/bioconductor-vulcan/meta.yaml

package bioconductor-vulcan

(downloads) docker_bioconductor-vulcan

Versions

1.4.0-0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-chippeakanno

>=3.16.0,<3.17.0

Depends bioconductor-csaw

>=1.16.0,<1.17.0

Depends bioconductor-deseq

>=1.34.0,<1.35.0

Depends bioconductor-diffbind

>=2.10.0,<2.11.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene

>=3.2.0,<3.3.0

Depends bioconductor-viper

>=1.16.0,<1.17.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-catools

Depends r-gplots

Depends r-locfit

Depends r-wordcloud

Depends r-zoo

Requirements

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>)