VegaMC

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

Bioconductor version: Release (2.14)

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 <sandro at ebi.ac.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("VegaMC")

To cite this package in a publication, start R and enter:

    citation("VegaMC")

Documentation

PDF R Script VegaMC
PDF   Reference Manual

Details

biocViews CopyNumberVariation, Software, aCGH
Version 3.2.0
In Bioconductor since BioC 2.10 (R-2.15)
License GPL-2
Depends R (>= 2.10.0), biomaRt, Biobase, genoset
Imports methods
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source VegaMC_3.2.0.tar.gz
Windows Binary VegaMC_3.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) VegaMC_3.2.0.tgz
Mac OS X 10.9 (Mavericks)
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