VegaMC
VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
Bioconductor version: Release (2.12)
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
| R Script | VegaMC | |
| Reference Manual |
Details
| biocViews | Bioinformatics, CopyNumberVariants, Software, aCGH |
| Version | 2.7.0 |
| 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_2.7.0.tar.gz |
| Windows Binary | VegaMC_2.7.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | VegaMC_2.7.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: webmaster@bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2013
