vulcan

This is the development version of vulcan; for the stable release version, see vulcan.

VirtUaL ChIP-Seq data Analysis using Networks

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology
Version	1.29.0
In Bioconductor since	BioC 3.6 (R-3.4) (7 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
System Requirements
URL

Suggests	vulcandata
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	vulcan_1.29.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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