CVE: Cancer Variant Explorer

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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]
Date of publication
None
Maintainer
Andreas Mock <mock.science@gmail.com>
License
GPL-3
Version
1.0.0

View on Bioconductor

Man pages

genes_WGCNA
Top 5000 most variant genes in TCGA RNAseq data
GS_lscore
Lymphocyte score gene significance (GS)
GS_pmet
Primary vs metastasis gene significance (GS)
GS_survival
Survival gene significance (GS)
GS_UV
UV signature gene significance (GS)
GS_Vem
Vemurafenib resistance gene significance (GS)
label_order
Label order of co-expression modules
METree_GO
Gene tree of co-expression network
MM
Module membership
modules
Module assignment of top 5000 most variant genes in TCGA...
MS_lscore_bar
Lymphocyte score module significance scaled for barplot
MS_pmet_bar
Primary vs metastasis module significance scaled for barplot
MS_survival_bar
Survival module significance scaled for barplot
MS_UV_bar
UV signature module significance scaled for barplot
MS_Vem_bar
Vemurafenib resistance module significance scaled for barplot
oncotator_example
Example Oncotator output for the case study described in the...
openCVE
Open Cancer Variant Explorer (CVE) Shiny app
WGCNAmelanoma_extension
Melanoma co-expression network CVE extension

Files in this package

CVE/DESCRIPTION
CVE/NAMESPACE
CVE/R
CVE/R/openCVE.R
CVE/README.md
CVE/build
CVE/build/vignette.rds
CVE/data
CVE/data/WGCNAmelanoma_extension.RData
CVE/data/datalist
CVE/data/oncotator_example.RData
CVE/inst
CVE/inst/Shiny
CVE/inst/Shiny/CVE
CVE/inst/Shiny/CVE/server.R
CVE/inst/Shiny/CVE/ui.R
CVE/inst/Shiny/CVE_WGCNA_melanoma
CVE/inst/Shiny/CVE_WGCNA_melanoma/server.R
CVE/inst/Shiny/CVE_WGCNA_melanoma/ui.R
CVE/inst/doc
CVE/inst/doc/CVE_tutorial.R
CVE/inst/doc/CVE_tutorial.Rmd
CVE/inst/doc/CVE_tutorial.html
CVE/inst/doc/WGCNA_from_TCGA_RNAseq.R
CVE/inst/doc/WGCNA_from_TCGA_RNAseq.Rmd
CVE/inst/doc/WGCNA_from_TCGA_RNAseq.html
CVE/man
CVE/man/GS_UV.Rd
CVE/man/GS_Vem.Rd
CVE/man/GS_lscore.Rd
CVE/man/GS_pmet.Rd
CVE/man/GS_survival.Rd
CVE/man/METree_GO.Rd
CVE/man/MM.Rd
CVE/man/MS_UV_bar.Rd
CVE/man/MS_Vem_bar.Rd
CVE/man/MS_lscore_bar.Rd
CVE/man/MS_pmet_bar.Rd
CVE/man/MS_survival_bar.Rd
CVE/man/WGCNAmelanoma_extension.Rd
CVE/man/genes_WGCNA.Rd
CVE/man/label_order.Rd
CVE/man/modules.Rd
CVE/man/oncotator_example.Rd
CVE/man/openCVE.Rd
CVE/tests
CVE/tests/testthat.R
CVE/vignettes
CVE/vignettes/CVE_tutorial.Rmd
CVE/vignettes/WGCNA_from_TCGA_RNAseq.Rmd