Man pages for mskilab/casereport
casereport: Whole-genome + transcription based report for cancer genomes
| annotated_bcf_to_oncotable | annotated_bcf_to_oncotable |
| annotate_pmkb_entries_as_tsg_or_onc | annotate_pmkb_entries_as_tsg_or_onc |
| annotate_with_pmkb | annotate_with_pmkb |
| check_file | check_file |
| check_GRanges_compatibility | check_GRanges_compatibility |
| circos | circos Quick utility function for circos plot with read... |
| cn.plot | cn.plot |
| compute_rna_quantiles | compute_rna_quantiles |
| counts.to.allele.cn | counts.to.allele.cn |
| covcbs | covcbs |
| create_genes_gtrack | create_genes_gtrack |
| create.summary | create.summary |
| deconstructsigs_histogram | deconstructsigs_histogram |
| extract_variant_types_from_pmkb | extract_variant_types_from_pmkb |
| filter.snpeff | filter.snpeff |
| fusion.plot | fusion.plot |
| fusion.table | fusion.table |
| fusion.wrapper | fusion.wrapper |
| gallery.wrapper | gallery.wrapper |
| get_gene_ampdel_annotations | zchoo Monday, May 03, 2021 02:42:51 PM |
| get_gene_copy_numbers | get_gene_copy_numbers |
| get_oncokb_annotations | get_oncokb_annotations |
| get_oncokb_gene_entry_url | get_oncokb_gene_entry_url |
| get_oncokb_response | get_oncokb_response |
| get_pmkb_dt | get_pmkb_dt |
| get_pmkb_tier_table | get_pmkb_tier_table |
| grab.agtrack | grab.agtrack |
| grab.gene.ranges | grab.gene.ranges |
| grab.hets | grab.hets |
| grab.window | grab.window |
| makeSummaryTable | makeSummaryTable |
| oncoprint | oncoprint |
| oncotable | oncotable |
| plot_expression_histograms | plot_expression_histograms |
| ppgrid | ppgrid |
| pp_plot | pp_plot |
| ridge.plot | ridge.plot |
| rna_quantile | rna_quantile |
| rna_reformat | rna_reformat |
| rna.waterfall.plot | rna.waterfall.plot |
| set_param | set_param |
| star2grl | star2grl Quick utility function to convert star-fusion... |
| summarize_cases | summarize_cases |
| sv.plot | sv.plot |
| test_oncokb_api | test_oncokb_api |
| wgs.circos | wgs.circos Quick utility function for circos plot with read... |
| wgs_gtrack | wgs_gtrack |
| wgs.report | wgs.report |
