vulcan
This is the released version of vulcan; for the devel version, see vulcan.
VirtUaL ChIP-Seq data Analysis using Networks
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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 |
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_1.34.0.tar.gz |
| Windows Binary (x86_64) | vulcan_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | vulcan_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | vulcan_1.34.0.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 |