From bb4182e6be9155d7c7deddc77870bc4c7df47010 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Fri, 14 Jun 2024 13:40:44 +0000 Subject: [PATCH] Built PCGR website: https://sigven.github.io/pcgr/ --- 404.html | 19 +- LICENSE-text.html | 13 +- LICENSE.html | 13 +- articles/CHANGELOG.html | 294 +++- articles/annotation_resources.html | 157 +- articles/developers.html | 23 +- articles/faq.html | 62 +- articles/index.html | 19 +- articles/input.html | 109 +- articles/installation.html | 288 ++-- articles/output.html | 1363 +++++++---------- articles/primary_tumor_sites.html | 60 +- .../crosstalk-1.1.1/css/crosstalk.css | 27 - .../crosstalk-1.2.1/css/crosstalk.min.css | 1 + .../js/crosstalk.js | 0 .../js/crosstalk.js.map | 0 .../js/crosstalk.min.js | 0 .../js/crosstalk.min.js.map | 0 .../crosstalk-1.2.1/scss/crosstalk.scss | 75 + .../datatables.js | 87 +- .../css/jquery.dataTables.min.css | 1 - .../js/jquery.dataTables.min.js | 192 --- .../css/jquery.dataTables.extra.css | 0 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.../bootstrap.bundle.min.js.map | 1 + deps/bootstrap-5.3.1/bootstrap.min.css | 5 + deps/data-deps.txt | 4 +- img/sc1.png | Bin 0 -> 944130 bytes img/sc2.png | Bin 0 -> 837200 bytes img/sc3.png | Bin 0 -> 1074159 bytes index.html | 60 +- pkgdown.js | 8 +- pkgdown.yml | 8 +- reference/af_distribution.html | 116 ++ reference/append_annotation_links.html | 28 +- .../append_cancer_association_ranks.html | 121 ++ ....html => append_cancer_gene_evidence.html} | 43 +- reference/append_dbmts_var_link.html | 20 +- reference/append_dbnsfp_var_link.html | 15 +- reference/append_drug_var_link.html | 32 +- reference/append_gwas_citation_phenotype.html | 29 +- reference/append_read_support.html | 126 -- ... => append_targeted_drug_annotations.html} | 42 +- reference/append_tcga_var_link.html | 21 +- reference/append_tfbs_annotation.html | 15 +- ...t_data_cna.html => assign_acmg_tiers.html} | 64 +- reference/assign_germline_popfreq_status.html | 27 +- reference/assign_mutation_type.html | 13 +- reference/assign_somatic_classification.html | 29 +- .../assign_somatic_germline_evidence.html | 24 +- reference/assign_tier1_tier2_acmg.html | 112 -- .../{pipe.html => biomarker_evidence.html} | 32 +- reference/cancer_phenotypes_regex.html | 13 +- reference/check_common_colnames.html | 18 +- ...ems_to_var.html => check_file_exists.html} | 49 +- reference/clinvar_germline_status.html | 21 +- reference/color_palette.html | 13 +- reference/cosmic_sbs_signatures.html | 105 ++ reference/cosmic_somatic_status.html | 18 +- reference/cpsr_acmg.html | 124 -- reference/data_coltype_defs.html | 101 ++ reference/data_integrity_check.html | 124 -- reference/dbsnp_germline_status.html | 22 +- reference/deduplicate_eitems.html | 21 +- reference/detect_vcf_sample_name.html | 21 +- reference/df_string_replace.html | 18 +- reference/dt_display.html | 101 ++ reference/effect_prediction_algos.html | 13 +- ...tions.html => expand_biomarker_items.html} | 52 +- reference/export_quarto_evars.html | 106 ++ reference/filter_eitems_by_site.html | 13 +- reference/filter_read_support.html | 20 +- reference/generate_annotation_link.html | 35 +- reference/generate_pcgr_report.html | 123 -- ...s_pheno_link.html => generate_report.html} | 48 +- ...l => generate_report_data_expression.html} | 35 +- reference/generate_report_data_kataegis.html | 13 +- reference/generate_report_data_msi.html | 31 +- reference/generate_report_data_rainfall.html | 18 +- ...l => generate_report_data_signatures.html} | 60 +- .../generate_report_data_signatures_mp.html | 130 -- reference/generate_report_data_snv_indel.html | 144 -- reference/generate_report_data_tmb.html | 37 +- reference/generate_report_data_trials.html | 18 +- reference/generate_tier_tsv.html | 13 +- reference/germline_filter_levels.html | 102 ++ reference/get_calls.html | 149 -- reference/get_clin_assocs_cna.html | 18 +- reference/get_clin_assocs_snv_indel.html | 126 -- reference/get_cna_cytoband.html | 110 -- ...it_cna_content.html => 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=> init_snv_indel_vstats.html} | 52 +- reference/init_tmb_content.html | 23 +- reference/init_tumor_only_content.html | 15 +- reference/init_valuebox_content.html | 106 -- reference/init_var_content.html | 13 +- reference/kataegis_detect.html | 18 +- reference/kataegis_input.html | 18 +- reference/load_all_eitems.html | 18 +- reference/load_dna_variants.html | 138 ++ reference/load_eitems.html | 24 +- ...s_states.html => load_expression_csq.html} | 31 +- ...nes.html => load_expression_outliers.html} | 44 +- reference/load_expression_similarity.html | 103 ++ reference/load_reference_data.html | 110 ++ ..._tumor_only.html => load_somatic_cna.html} | 48 +- reference/load_somatic_snv_indel.html | 114 ++ ...determine_genotype.html => load_yaml.html} | 41 +- reference/log4r_debug.html | 13 +- reference/log4r_fatal.html | 103 ++ reference/log4r_info.html | 13 +- reference/log4r_warn.html | 13 +- reference/log_var_eitem_stats.html | 18 +- reference/make_cnaqc_object.html | 111 ++ reference/max_af_gnomad.html | 18 +- reference/max_af_onekg.html | 112 -- reference/msi_indel_fraction_plot.html | 18 +- reference/msi_indel_load_plot.html | 117 ++ reference/order_variants.html | 18 +- reference/pkg_exists.html | 13 +- reference/plot_tmb_primary_site_tcga.html | 45 +- reference/plot_value_boxes.html | 18 +- reference/pon_status.html | 21 +- reference/predict_msi_status.html | 23 +- reference/qc_var_eitems.html | 41 +- reference/recode_logical_vars.html | 112 -- reference/remove_cols_from_df.html | 13 +- reference/set_report_metadata.html | 134 -- reference/sort_chromosomal_segments.html | 18 +- ...anel_display_html.html => strip_html.html} | 40 +- reference/structure_var_eitems.html | 18 +- ...sc_segment_link.html => tcga_cohorts.html} | 57 +- reference/tcga_somatic_status.html | 18 +- reference/tidyeval.html | 13 +- reference/tier_af_distribution.html | 20 +- reference/tsv_cols.html | 101 ++ reference/update_maf_allelic_support.html | 118 -- reference/update_report.html | 21 +- reference/upset_plot_tumor_only.html | 118 -- reference/variant_db_url.html | 13 +- reference/variant_stats_report.html | 41 +- reference/write_processed_vcf.html | 20 +- reference/write_report_excel.html | 103 ++ reference/write_report_output.html | 136 -- reference/write_report_quarto_html.html | 103 ++ ...a_value_box.html => write_report_tsv.html} | 61 +- search.json | 2 +- sitemap.xml | 171 +-- 194 files changed, 5072 insertions(+), 6394 deletions(-) delete mode 100644 articles/primary_tumor_sites_files/crosstalk-1.1.1/css/crosstalk.css create mode 100644 articles/primary_tumor_sites_files/crosstalk-1.2.1/css/crosstalk.min.css rename articles/primary_tumor_sites_files/{crosstalk-1.1.1 => crosstalk-1.2.1}/js/crosstalk.js (100%) rename articles/primary_tumor_sites_files/{crosstalk-1.1.1 => crosstalk-1.2.1}/js/crosstalk.js.map (100%) rename articles/primary_tumor_sites_files/{crosstalk-1.1.1 => crosstalk-1.2.1}/js/crosstalk.min.js (100%) rename 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deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map create mode 100644 deps/bootstrap-5.3.1/bootstrap.min.css create mode 100644 img/sc1.png create mode 100644 img/sc2.png create mode 100644 img/sc3.png create mode 100644 reference/af_distribution.html create mode 100644 reference/append_cancer_association_ranks.html rename reference/{get_proper_maf_alleles.html => append_cancer_gene_evidence.html} (62%) delete mode 100644 reference/append_read_support.html rename reference/{targeted_drugs_pr_ttype.html => append_targeted_drug_annotations.html} (61%) rename reference/{generate_report_data_cna.html => assign_acmg_tiers.html} (59%) delete mode 100644 reference/assign_tier1_tier2_acmg.html rename reference/{pipe.html => biomarker_evidence.html} (60%) rename reference/{match_eitems_to_var.html => check_file_exists.html} (50%) create mode 100644 reference/cosmic_sbs_signatures.html delete mode 100644 reference/cpsr_acmg.html create mode 100644 reference/data_coltype_defs.html delete mode 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100644 reference/write_report_output.html create mode 100644 reference/write_report_quarto_html.html rename reference/{generate_report_data_value_box.html => write_report_tsv.html} (56%) diff --git a/404.html b/404.html index 723fa769..044e166f 100644 --- a/404.html +++ b/404.html @@ -13,10 +13,10 @@ - - + + - + License • PCGRLicense • PCGR Skip to contents -