Man pages for ys-amms/bionexr
Integrative network-based analysis of cancer somatic mutation and expression data
| firehose_get | Main function for downloading data from firehose. |
| hnsc_exp_part | Example data |
| hnsc_expressed_genes | Example data |
| hnsc_mut_part | Example data |
| identify_expressed_genes | Identify expressed genes. Identify expressed genes based on... |
| list_cohorts | List available cohorts on firehose website. |
| list_runs | List available runs on firehose website. |
| list_run_types | List available run types on firehose website. |
| network_from_ppi | Generate network from PPI-based result. |
| network_from_significant_branches | Generate network from pathway branches. |
| perform_gene_pathway | Perform gene module of pathway-based approach. |
| perform_gene_ppi | Perform gene module of PPI-based approach. |
| perform_main_pathway | Pipeline of pathway-based analysis. |
| perform_main_ppi | Pipeline of PPI-based analysis. |
| perform_network_pathway | Perform network module of pathway-based approach. |
| perform_network_ppi | Perform network module of PPI-based approach. |
| plot_pathway | visualize pathway-based network. |
| plot_ppi | visualize PPI-based network. |
| prepare_ma | Prepare mutation assessor dataset. |
