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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("VegaMC")
AuthorS. Morganella and M. Ceccarelli
Bioconductor views CopyNumberVariation aCGH
Date of publicationNone
MaintainerSandro Morganella <morganellaalx@gmail.com>
LicenseGPL-2
Version3.14.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/createHTML.R R/getGenes.R R/qvalue.R R/sortData.R R/vegaMC.R
build
build/vignette.rds
inst
inst/doc
inst/doc/VegaMC.R
inst/doc/VegaMC.Rnw
inst/doc/VegaMC.pdf
inst/example
inst/example/breast_Affy500K.txt
inst/scripts
inst/scripts/sorttable.js
inst/template
inst/template/AberrantGeneTableRow.html
inst/template/AberrantRegionTableRow.html
inst/template/AllRegionTableRow.html
inst/template/Footer.html
inst/template/FooterTable.html
inst/template/HeaderGenes.html
inst/template/HeaderRegions.html
inst/template/HeaderTableAberrantGenes.html
inst/template/HeaderTableAberrantRegions.html
inst/template/HeaderTableAllRegions.html
inst/template/InputParameters.html
inst/template/image
inst/template/image/bioinfologo.png
inst/template/image/ensemblicon.gif
man
man/VegaMC-package.Rd man/sortData.Rd man/vegaMC-methods.Rd
src
src/run_vegaMC.c
src/sort_data.c
src/vegaMC.c
vignettes
vignettes/VegaMC.Rnw

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