To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CVE")

In most cases, you don't need to download the package archive at all.

CVE

DOI: 10.18129/B9.bioc.CVE    

Cancer Variant Explorer

Bioconductor version: Release (3.6)

Shiny app for interactive variant prioritisation in precision oncology. The input file for CVE is the output file of the recently released Oncotator Variant Annotation tool summarising variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive priortisation in CVE is based on known germline and cancer variants, DNA repair genes and functional prediction scores. An optional feature of CVE is the exploration of the tumour-specific pathway context that is facilitated using co-expression modules generated from publicly available transcriptome data. Finally druggability of prioritised variants is assessed using the Drug Gene Interaction Database (DGIdb).

Author: Andreas Mock [aut, cre]

Maintainer: Andreas Mock <mock.science at gmail.com>

Citation (from within R, enter citation("CVE")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("CVE")

Documentation

HTML R Script Cancer Variant Explorer (CVE) tutorial
HTML R Script Weighted gene co-expression network analysis with TCGA RNAseq data
PDF   Reference Manual

Details

biocViews BiomedicalInformatics, Software
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL-3
Depends R (>= 3.4.0)
Imports shiny, ConsensusClusterPlus, RColorBrewer, gplots, plyr, ggplot2, jsonlite, ape, WGCNA
LinkingTo
Suggests knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package CVE_1.4.0.tar.gz
Windows Binary CVE_1.4.0.zip
Mac OS X 10.11 (El Capitan) CVE_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CVE
Package Short Url http://bioconductor.org/packages/CVE/
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