CVE

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CVE.

Cancer Variant Explorer


Bioconductor version: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CVE")

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

Details

biocViews BiomedicalInformatics, Software
Version 1.6.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.4.0)
Imports shiny, ConsensusClusterPlus, RColorBrewer, gplots, plyr, ggplot2, jsonlite, ape, WGCNA
System Requirements
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Suggests knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
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Package Archives

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

Source Package CVE_1.6.0.tar.gz
Windows Binary CVE_1.6.0.zip
Mac OS X 10.11 (El Capitan) CVE_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CVE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CVE
Package Short Url https://bioconductor.org/packages/CVE/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive