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VegaMC

VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

Bioconductor version: Release (3.17)

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 (from within R, enter citation("VegaMC")):

Installation

To install this package, start R (version "4.3") 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 PDF R Script
Reference Manual PDF

Details

biocViews CopyNumberVariation, Software, aCGH
Version 3.38.0
In Bioconductor since BioC 2.10 (R-2.15) (11.5 years)
License GPL-2
Depends R (>= 2.10.0), biomaRt, Biobase
Imports methods
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package VegaMC_3.38.0.tar.gz
Windows Binary VegaMC_3.38.0.zip (64-bit only)
macOS Binary (x86_64) VegaMC_3.38.0.tgz
macOS Binary (arm64) VegaMC_3.38.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/VegaMC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VegaMC
Bioc Package Browser https://code.bioconductor.org/browse/VegaMC/
Package Short Url https://bioconductor.org/packages/VegaMC/
Package Downloads Report Download Stats