CVE

DOI: 10.18129/B9.bioc.CVE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CVE.

Cancer Variant Explorer

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL-3
Depends	R (>= 3.4.0), tidyverse, plyr, ggplot2
Imports	shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite, ape, WGCNA
LinkingTo
Suggests	knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CVE_1.8.0.tar.gz
Windows Binary	CVE_1.8.0.zip
Mac OS X 10.11 (El Capitan)	CVE_1.8.0.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	http://bioconductor.org/packages/CVE/
Package Downloads Report	Download Stats