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vulcan

VirtUaL ChIP-Seq data Analysis using Networks


Bioconductor version: Release (3.18)

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.

Author: Federico M. Giorgi, Andrew N. Holding, Florian Markowetz

Maintainer: Federico M. Giorgi <federico.giorgi at gmail.com>

Citation (from within R, enter citation("vulcan")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("vulcan")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("vulcan")
Vulcan: VirtUaL ChIP-Seq Analysis through Networks PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License LGPL-3
Depends R (>= 4.0), ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
Imports wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq2, Biobase
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package vulcan_1.24.0.tar.gz
Windows Binary vulcan_1.24.0.zip
macOS Binary (x86_64) vulcan_1.24.0.tgz
macOS Binary (arm64) vulcan_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/vulcan
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/vulcan
Bioc Package Browser https://code.bioconductor.org/browse/vulcan/
Package Short Url https://bioconductor.org/packages/vulcan/
Package Downloads Report Download Stats