# Cancer Variant Explorer

## Documentation for package ‘CVE’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help 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 RNAseq data
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 paper
openCVE | Open Cancer Variant Explorer (CVE) Shiny app
WGCNAmelanoma_extension | Melanoma co-expression network CVE extension