VegaMC
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see VegaMC.
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
Bioconductor version: 3.9
This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.
Author: S. Morganella and M. Ceccarelli
Maintainer: Sandro Morganella <morganellaalx at gmail.com>
citation("VegaMC")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("VegaMC")
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("VegaMC")| VegaMC | R Script | |
| Reference Manual |
Details
| biocViews | CopyNumberVariation, Software, aCGH |
| Version | 3.22.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12 years) |
| License | GPL-2 |
| Depends | R (>= 2.10.0), biomaRt, Biobase |
| Imports | methods, genoset |
| System Requirements | |
| URL |
See More
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| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | VegaMC_3.22.0.tar.gz |
| Windows Binary | VegaMC_3.22.0.zip |
| Mac OS X 10.11 (El Capitan) | VegaMC_3.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VegaMC |
| Source Repository (Developer Access) | git clone [email protected]:packages/VegaMC |
| Bioc Package Browser | https://code.bioconductor.org/browse/VegaMC/ |
| Package Short Url | https://bioconductor.org/packages/VegaMC/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |