API for mskilab/casereport
casereport: Whole-genome + transcription based report for cancer genomes
| Global functions | |
|---|---|
| annotate_germline_mutations | Source code |
| annotate_pmkb_entries_as_tsg_or_onc | Man page |
| annotate_with_pmkb | Man page |
| annotated_bcf_to_oncotable | Man page |
| check_GRanges_compatibility | Man page |
| check_file | Man page |
| circos | Man page |
| cn.plot | Man page |
| compute_rna_quantiles | Man page |
| counts.to.allele.cn | Man page |
| covcbs | Man page Source code |
| create.summary | Man page |
| create_genes_gtrack | Man page Source code |
| deconstructsigs_histogram | Man page |
| dlrs | Source code |
| extract_variant_types_from_pmkb | Man page |
| filter.snpeff | Man page |
| fusion.plot | Man page |
| fusion.table | Man page |
| fusion.wrapper | Man page |
| gallery.wrapper | Man page Source code |
| get_gene_ampdel_annotations | Man page |
| get_gene_copy_numbers | Man page |
| get_oncokb_annotations | Man page |
| get_oncokb_gene_entry_url | Man page |
| get_oncokb_response | Man page |
| get_pmkb_dt | Man page Source code |
| get_pmkb_tier_table | Man page Source code |
| grab.agtrack | Man page |
| grab.gene.ranges | Man page |
| grab.hets | Man page |
| grab.window | Man page Source code |
| makeSummaryTable | Man page |
| oncoprint | Man page |
| oncotable | Man page |
| panel.fun | Source code |
| plot_expression_histograms | Man page |
| pp_plot | Man page |
| ppgrid | Man page |
| process_germline_muts | Source code |
| rel2abs | Source code |
| ridge.plot | Man page |
| rna.waterfall.plot | Man page |
| rna_quantile | Man page |
| rna_reformat | Man page |
| set_param | Man page |
| star2grl | Man page Source code |
| summarize_cases | Man page |
| sv.plot | Man page |
| test_oncokb_api | Man page |
| wgs.circos | Man page Source code |
| wgs.report | Man page Source code |
| wgs_gtrack | Man page |
