DOI: 10.18129/B9.bioc.vulcan    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see vulcan.

VirtUaL ChIP-Seq data Analysis using Networks

Bioconductor version: 3.10

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>

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


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


biocViews ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology
Version 1.8.0
In Bioconductor since BioC 3.6 (R-3.4) (2.5 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
Suggests vulcandata
Depends On Me
Imports Me
Suggests Me flowSpecs
Links To Me
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