Package Recipe 'bioconductor-vulcan'

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:

1.32.0-0, 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,

1.32.0-0, 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:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-chippeakanno >=3.44.0,<3.45.0
on bioconductor-csaw >=1.44.0,<1.45.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-diffbind >=3.20.0,<3.21.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.22.0,<3.23.0
on bioconductor-viper >=1.44.0,<1.45.0
on r-base >=4.5,<4.6.0a0
on r-catools
on r-gplots
on r-locfit
on r-wordcloud
on r-zoo

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-vulcan

to add into an existing workspace instead, run:

pixi add bioconductor-vulcan

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-vulcan

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-vulcan

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-vulcan/README.html)