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| 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 |