CVE: Cancer Variant Explorer

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CVE")
AuthorAndreas Mock [aut, cre]
Bioconductor views BiomedicalInformatics
Date of publicationNone
MaintainerAndreas Mock <mock.science@gmail.com>
LicenseGPL-3
Version1.2.0

View on Bioconductor

Functions

crcCase Man page
genes_WGCNA Man page
get.oncotator.anno Man page
GS_lscore Man page
GS_pmet Man page
GS_survival Man page
GS_UV Man page
GS_Vem Man page
label_order Man page
melanomaCase Man page
METree_GO Man page
MM Man page
modules Man page
MS_lscore Man page
MS_lscore_bar Man page
MS_pmet Man page
MS_pmet_bar Man page
MS_survival Man page
MS_survival_bar Man page
MS_UV Man page
MS_UV_bar Man page
MS_vem Man page
MS_Vem_bar Man page
openCVE Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.