vulcan
This is the development version of vulcan; for the stable release version, see vulcan.
All Bioconductor versions of vulcan
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
VirtUaL ChIP-Seq data Analysis using Networks
Bioconductor version: 3.24 · Package version: 1.35.1
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 [aut, cre], Andrew N. Holding [aut], Florian Markowetz [aut]
Maintainer: Federico M. Giorgi <federico.giorgi at gmail.com>
Citation
From within R, enter citation("vulcan"):
Federico M. Giorgi, Andrew N. Holding, Florian Markowetz. vulcan: VirtUaL ChIP-Seq data Analysis using Networks. doi:10.18129/B9.bioc.vulcan, R package version 1.35.1, https://bioconductor.org/packages/vulcan.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("vulcan")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.35.1 |
| License | LGPL-3 |
| Last updated | 2026-08-17 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 1496 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/vulcan/ |
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | vulcan_1.35.1.tar.gz |
| Windows binary (x86_64) | vulcan_1.35.1.zip |
| macOS binary (arm64) | vulcan_1.35.1.tgz |
| macOS binary (x86_64) | vulcan_1.35.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/vulcan |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/vulcan |
| Package Downloads Report | Download Stats |
Dependencies
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, SummarizedExperiment
Suggests: vulcandata