vulcan

DOI: 10.18129/B9.bioc.vulcan  

VirtUaL ChIP-Seq data Analysis using Networks

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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

Details

biocViews	ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 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
LinkingTo
Suggests	vulcandata
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	vulcan_1.20.0.tar.gz
Windows Binary	vulcan_1.20.0.zip
macOS Binary (x86_64)	vulcan_1.20.0.tgz
macOS Binary (arm64)	vulcan_1.20.0.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