To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CVE")
In most cases, you don't need to download the package archive at all.
CVE
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see CVE.
Cancer Variant Explorer
Bioconductor version: 3.4
Shiny app for interactive variant prioritisation in precision cancer medicine. 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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CVE")
Documentation
| HTML | R Script | Cancer Variant Explorer (CVE) tutorial |
| HTML | R Script | Weighted gene co-expression network analysis with TCGA RNAseq data |
| Reference Manual |
Details
| biocViews | BiomedicalInformatics, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (0.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.3), shiny, ConsensusClusterPlus, RColorBrewer, gplots, plyr, ggplot2, jsonlite, ape, WGCNA |
| Imports | |
| LinkingTo | |
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CVE_1.0.0.tar.gz |
| Windows Binary | CVE_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | CVE_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CVE/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CVE/ |
| Package Downloads Report | Download Stats |
Documentation »
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