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>

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

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

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