vulcan

DOI: 10.18129/B9.bioc.vulcan    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see vulcan.

VirtUaL ChIP-Seq data Analysis using Networks

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	Vulcan: VirtUaL ChIP-Seq Analysis through Networks
PDF		Reference Manual
Text		NEWS

Details

biocViews	ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology
Version	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	LGPL-3
Depends	R (>= 3.4), ChIPpeakAnno, TxDb.Hsapiens.UCSC.hg19.knownGene, zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
Imports	wordcloud, csaw, gplots, stats, utils, caTools, graphics, DESeq, Biobase
LinkingTo
Suggests	vulcandata
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	vulcan_1.6.0.tar.gz
Windows Binary	vulcan_1.6.0.zip
Mac OS X 10.11 (El Capitan)	vulcan_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/vulcan
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/vulcan
Package Short Url	https://bioconductor.org/packages/vulcan/
Package Downloads Report	Download Stats