Man pages for sbenfatto/PARIS
PAn-canceR Inferred Synthetic lethalities (PARIS), a machine learning-based approach to predict cancer vulnerabilities
| add_group | Add group to Pairs file |
| add_imp_scores | Merge selected gene pairs with their importance scores |
| add_imp_scores_loop | Merge selected gene pairs with their importance scores |
| compute_interaction_freq | Calculate fraction of interacting gene pairs over total |
| filter_essential_genes | Filter essential genes |
| get_paralog_biomart | Retrieve Paralogs from gene vector |
| get_stringdb_interactions | Retrieve StringDB interactions for gene pairs |
| HTBreaks | Compute and plot HTBreaks |
| HTBreaks_hist | Compute and plot HTBreaks + histogram |
| load_imp_scores | Load importance scores |
| load_imp_scores2 | Load importance scores |
| myinfo | Info data. |
| mynewcn | Copy number data. |
| mynewexp | Expression data. |
| mynewmerge | Dependency data. |
| mynewmut | Mutation data. |
| mystat | Stats data. |
| plotboruta | plot Boruta top 10 features |
| plot_box_def_dep | Plot boxplot dependecy vs deficient |
| plot_box_mut_dep | Plot boxplot dependecy vs mutation |
| plot_common_pairs | Plot scatterplot Gini corrected vs raw permutation for a... |
| plot_mut_dep | Plot boxplot dependecy vs mutation |
| plot_rank_def_exp_dep | Plot ranked barplot dependecy score, colored by expression... |
| plot_rank_def_ratio_dep | Plot ranked barplot dependecy score, colored by ratio... |
| plot_rank_def_ratio_dep_by_disease | Plot ranked barplot dependecy score, colored by ratio... |
| plot_rank_exp_dep | Plot rank dependecy vs expression |
| plot_rank_exp_dep_sub | Plot rank dependecy vs expression |
| plot_rank_mut_dep | Plot rank dependecy vs mutation |
| plot_rank_mut_dep_sub | Plot rank dependecy vs mutation |
| plot_sca_exp_dep | Plot scatterplot dependecy vs expression |
| plot_sca_exp_dep_ratio | Plot scatterplot dependecy vs ratio expression |
| plot_sca_mut_dep | Plot scatterplot dependecy vs mutation |
| plot_stringdb_interactions_by_group | Plot percentage of interacting gene over total |
| plot_stringdb_interactions_combined_score_by_group | Plot StringDB combined scores |
| plot_top_rank | Plot top rank selected genes pairs |
| plot_top_rank_color | Plot top rank selected genes pairs colored |
| plot_upset | Upsetplot |
| plot_vl_mut_dep | Plot violin dependecy vs mutation |
| RF_exp | Random Forest Feature Selection - Genes expression ->... |
| RF_mut | Random Forest Feature Selection - Mutated genes -> Dependent... |
| run_PARIS | Main function to run PARIS pipeline |
| scale01 | Scaling function |
| select_pairs | Read selected gene pairs from a directory |
| select_pairs2 | Read selected gene pairs from a directory |
| subset_by_threshold | Subset a dataframe of gene pairs by threshold |
