Package: CVE
Title: Cancer Variant Explorer
Version: 1.8.0
Authors@R: person("Andreas", "Mock", email = "mock.science@gmail.com", role = c("aut", "cre"))
Author: Andreas Mock [aut, cre]
Maintainer: Andreas Mock <mock.science@gmail.com>
Description: 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).
Depends: R (>= 3.4.0), tidyverse, plyr, ggplot2
Imports: shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite,
        ape, WGCNA
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
VignetteBuilder: knitr
biocViews: BiomedicalInformatics
git_url: https://git.bioconductor.org/packages/CVE
git_branch: RELEASE_3_8
git_last_commit: 3985d5c
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: no
Packaged: 2018-10-31 03:09:59 UTC; biocbuild
Built: R 3.5.1; ; 2018-10-31 10:59:02 UTC; windows
