API for rdocking/amlpmpsupport
Support Functions for AML PMP RNA-Seq Stratification Manuscript
| Global functions | |
|---|---|
| %>% | Man page |
| add_colour_vector_to_concordance | Man page Source code |
| apply_eln2015_cyto | Man page Source code |
| apply_eln2017_cyto | Man page Source code |
| apply_eln2017_rna | Man page Source code |
| apply_expression_signature_reclassification | Man page Source code |
| aps_volcano_plot | Man page Source code |
| calculate_reference_set_coefficient_of_variation | Man page Source code |
| calculate_reference_set_mean_expression | Man page Source code |
| connect_to_aml_project_orm | Man page Source code |
| construct_rna_qc_dataframe | Man page Source code |
| construct_sailfish_gene_dataframe | Man page Source code |
| convert_sailfish_df_to_matrix | Man page Source code |
| density_plotter | Man page Source code |
| downregulated_genes | Man page Source code |
| eng_log_breaks | Man page Source code |
| expression_matrix_to_long_df | Man page Source code |
| expression_summary | Man page Source code |
| fit_coxph | Man page Source code |
| gather_expression_matrix_to_tidy_df | Man page Source code |
| get_cluster_assignments_for_k | Man page Source code |
| ggsave_pdf_and_png | Man page Source code |
| grid_arrange_shared_legend | Man page Source code |
| group_tally_table | Man page Source code |
| hit_plotter | Man page Source code |
| limma_logFC_to_signed_foldchange | Man page Source code |
| log2_plus1_transform | Man page Source code |
| long_df_to_ranked_matrix | Man page Source code |
| matrix_glimpse | Man page Source code |
| munge_voom_to_ipa | Man page Source code |
| nest_libraries_by_patient | Man page Source code |
| num_to_text | Man page Source code |
| parse_pavfinder_0.2.0 | Man page |
| parse_pavfinder_0.3.0 | Man page |
| pathway_enrichment_plot | Man page Source code |
| plot_heatmap_for_k | Man page Source code |
| plot_rf_predictions | Man page Source code |
| plot_survival | Man page Source code |
| plot_vars_by_coverage | Man page Source code |
| plot_vars_by_vaf | Man page Source code |
| pretty_kable | Man page Source code |
| pretty_num | Man page Source code |
| pull_enrichr_enriched_terms | Man page Source code |
| pull_enrichr_terms_to_plot | Man page Source code |
| random_forest_summary | Man page Source code |
| read_filled_variant_tsv | Man page Source code |
| rescale_genes_by_reference | Man page Source code |
| retrieve_db_comments | Man page Source code |
| retrieve_db_curated_results | Man page Source code |
| retrieve_db_libraries | Man page Source code |
| retrieve_db_paths | Man page Source code |
| retrieve_db_specimens | Man page Source code |
| rf_predictions | Man page Source code |
| rna_seqc_parser | Man page |
| run_cna_workflow | Man page Source code |
| run_gage_for_feature | Man page Source code |
| run_voom_for_feature | Man page Source code |
| sailfish_gene_parser_post_0.7.0 | Man page |
| sailfish_isoform_parser_post_0.7.0 | Man page |
| sailfish_isoform_parser_pre_0.7.0 | Man page |
| scale_by_rolling_mean | Man page Source code |
| select_by_position | Man page Source code |
| split_gatk_format_vals | Man page Source code |
| spread_expression_df_to_matrix | Man page Source code |
| spread_filled_snv_df_to_wide | Man page Source code |
| subset_genes_by_thresholds | Man page Source code |
| subset_genes_for_plots | Man page Source code |
| subset_heatmap | Man page Source code |
| subset_pc_plot | Man page Source code |
| subtype_to_disease | Man page Source code |
| tfl_split_sort | Man page Source code |
| train_caret_rf | Man page Source code |
| upregulated_genes | Man page Source code |
| volcano_plotter | Man page Source code |
