To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("vulcan")

In most cases, you don't need to download the package archive at all.

vulcan

DOI: 10.18129/B9.bioc.vulcan    

VirtUaL ChIP-Seq data Analysis using Networks

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("vulcan")

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 1.0.0
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
Build Report  

Package Archives

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

Source Package vulcan_1.0.0.tar.gz
Windows Binary vulcan_1.0.0.zip
Mac OS X 10.11 (El Capitan) vulcan_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/vulcan
Package Short Url http://bioconductor.org/packages/vulcan/
Package Downloads Report Download Stats

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