vulcan
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see vulcan.
VirtUaL ChIP-Seq data Analysis using Networks
Bioconductor version: 3.12
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("vulcan")):
Installation
To install this package, start R (version "4.0") 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")| Vulcan: VirtUaL ChIP-Seq Analysis through Networks | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, GeneExpression, NetworkEnrichment, Software, SystemsBiology |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
| System Requirements | |
| URL |
See More
| 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_1.12.0.tar.gz |
| Windows Binary | vulcan_1.12.0.zip |
| macOS 10.13 (High Sierra) | vulcan_1.12.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |