CVE: Cancer Variant Explorer

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).

AuthorAndreas Mock [aut, cre]
Date of publicationNone
MaintainerAndreas Mock <mock.science@gmail.com>
LicenseGPL-3
Version1.0.0

View on Bioconductor

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

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

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