# Cancer Variant Explorer

## Documentation for package ‘CVE’ version 1.10.0

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

## Help Pages

crcCase | Example Oncotator output for the single-patient colorectal cancer sample
genes_WGCNA | Top 5000 most variant genes in TCGA RNAseq data
get.oncotator.anno | Open Cancer Variant Explorer (CVE) Shiny app
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
melanomaCase | Example Oncotator output for the melanoma cohort study described in the paper
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 | Lymphocyte score module significance (MS)
MS_lscore_bar | Lymphocyte score module significance scaled for barplot
MS_pmet | Primary vs metastasis module significance (MS)
MS_pmet_bar | Primary vs metastasis module significance scaled for barplot
MS_survival | Survival module significance (MS)
MS_survival_bar | Survival module significance scaled for barplot
MS_UV | UV signature module significance (MS)
MS_UV_bar | UV signature module significance scaled for barplot
MS_vem | Vemurafenib resistance module significance (MS)
MS_Vem_bar | Vemurafenib resistance module significance scaled for barplot
openCVE | Open Cancer Variant Explorer (CVE) Shiny app