CVE
This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CVE.
Cancer Variant Explorer
DOI: 10.18129/B9.bioc.CVE
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>
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")
Details
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Follow Installation instructions to use this package in your R session.