CVE
This package is for version 3.9 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: 3.9
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 "3.6") 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 |
Details
| biocViews | BiomedicalInformatics, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4.0), tidyverse, plyr, ggplot2 |
| Imports | shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite, ape, WGCNA |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CVE_1.10.0.tar.gz |
| Windows Binary | CVE_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | CVE_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CVE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CVE |
| Bioc Package Browser | https://code.bioconductor.org/browse/CVE/ |
| Package Short Url | https://bioconductor.org/packages/CVE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |