recipe bioconductor-vulcan

VirtUaL ChIP-Seq data Analysis using Networks

Homepage:

https://bioconductor.org/packages/3.20/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:

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  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:

>=2.66.0,<2.67.0

depends bioconductor-chippeakanno:

>=3.40.0,<3.41.0

depends bioconductor-csaw:

>=1.40.0,<1.41.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-diffbind:

>=3.16.0,<3.17.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends bioconductor-viper:

>=1.40.0,<1.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-catools:

depends r-gplots:

depends r-locfit:

depends r-wordcloud:

depends r-zoo:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-vulcan

and update with::

   mamba update bioconductor-vulcan

To create a new environment, run:

mamba create --name myenvname bioconductor-vulcan

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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