recipe bioconductor-vulcan

VirtUaL ChIP-Seq data Analysis using Networks

Homepage

https://bioconductor.org/packages/3.14/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

1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-chippeakanno >=3.28.0,<3.29.0

• bioconductor-csaw >=1.28.0,<1.29.0

• bioconductor-deseq2 >=1.34.0,<1.35.0

• bioconductor-diffbind >=3.4.0,<3.5.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

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

• bioconductor-viper >=1.28.0,<1.29.0

• r-base >=4.1,<4.2.0a0

• 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>)

Download stats

Link to this page

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