Man pages for umccr/gpgr
Genomics Platform Group Reporting
| abbreviate_effect | Abbreviate SV Effects |
| af_summary | umccrise AF summary |
| bcftools_stats_plot | Parse bcftools stats File |
| cancer_rmd | Generate UMCCR Cancer Report |
| count_pieces | Count Number of Parts in a String |
| date_log | Print current timestamp for logging |
| dragen_hrd | Parse DRAGEN HRD File |
| EFFECT_ABBREVIATIONS | Abbreviations for SV effects |
| get_oncokb_genes | Get OncoKB Genes From Somewhere |
| gpgr-package | gpgr: Genomics Platform Group Reporting |
| hrd_results_tabs | HRDetect and CHORD Summary Table |
| is_vcf | Does the input file look like a VCF? |
| mkdir | Create directory |
| pkg_exists | Does R Package Exist |
| plot_bnd_sr_pr_tot_hist | Histogram for SR, PR and SR + PR for BNDs |
| plot_bnd_sr_pr_tot_lines | Line plot for SR, PR and SR + PR for BNDs |
| process_cnv_tsv | Process CNV TSV |
| process_sv | Process SV TSV |
| purple_cnv_som_gene_process | Process PURPLE CNV Gene File for UMCCRISE |
| purple_cnv_som_gene_read | Read PURPLE CNV Gene File |
| purple_cnv_som_process | Process PURPLE CNV Somatic File for UMCCRISE |
| purple_cnv_som_read | Read PURPLE CNV Somatic File |
| purple_kataegis | Get PURPLE Kataegis Regions |
| purple_purity_read | Read PURPLE Purity file |
| purple_qc_read | Read PURPLE QC file |
| purple_snv_vcf_read | Read PURPLE Somatic SNV VCF |
| read_oncokb | Read OncoKB |
| session_info_kable | Session Information Kable |
| split_double_col | Split Two-Field Column |
| tidyeval | Tidy eval helpers |
| tsv_is_empty | Does the TSV file contain any non-header rows? |
| vcf_is_empty | Does the VCF file contain any variants? |
| virusbreakend_summary_read | Read VIRUSBreakend Summary File |
| virusbreakend_vcf_read | Read VIRUSBreakend VCF File |
| write_jsongz | Write gzipped JSON |
| write_tsvgz | Write a data frame to a tab delimited gzipped file |
| write_tsvjsongz | Write a data frame to gzipped TSV and JSON files |
