├── .Rbuildignore ├── .bumpversion.toml ├── .github ├── .gitignore └── workflows │ └── build_conda.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── bsicons.R ├── classification.R ├── data.R ├── input_data.R ├── main.R ├── plot.R ├── predisposition_gene.R ├── utils.R └── utils_shortcuts.R ├── README.md ├── conda ├── env │ └── yml │ │ ├── condabuild_env.yml │ │ └── pkgdown.yml └── recipe │ └── cpsr │ ├── build.sh │ └── meta.yaml ├── cpsr.Rproj ├── data-raw ├── acmg_evidence.tsv └── data-raw.R ├── data ├── acmg.rda ├── col_format_output.rda ├── color_palette.rda └── report_color.rda ├── inst ├── CITATION ├── examples │ ├── example.vcf.gz │ ├── example.vcf.gz.tbi │ └── example_custom_targets.tsv ├── extdata │ ├── CPSR_classification_score_thresholds.png │ ├── logo.png │ └── panel_zero.tsv.gz └── templates │ ├── cpsr.css │ ├── cpsr_bibliography.bib │ ├── cpsr_report.Rmd │ ├── cpsr_report.qmd │ ├── cpsr_theme.scss │ ├── favicon-16x16.png │ ├── quarto │ ├── cpsr_biomarkers.qmd │ ├── cpsr_classification.qmd │ ├── cpsr_documentation.qmd │ ├── cpsr_gwas.qmd │ ├── cpsr_pgx.qmd │ ├── cpsr_secondary_findings.qmd │ ├── cpsr_settings.qmd │ ├── cpsr_summary.qmd │ └── cpsr_virtual_panel.qmd │ └── rmarkdown │ ├── cpsr_biomarkers.Rmd │ ├── cpsr_documentation.Rmd │ ├── cpsr_gwas.Rmd │ ├── cpsr_secondary_findings.Rmd │ ├── cpsr_settings.Rmd │ ├── cpsr_summary.Rmd │ ├── cpsr_tiers.Rmd │ └── cpsr_virtual_panel.Rmd ├── man ├── acmg.Rd ├── append_cpg_properties.Rd ├── assign_classification.Rd ├── assign_pathogenicity_evidence.Rd ├── bs_icon2.Rd ├── check_variant2cancer_phenotype.Rd ├── col_format_output.Rd ├── color_palette.Rd ├── combine_novel_and_preclassified.Rd ├── exclude_vars_by_maf.Rd ├── exclude_vars_non_cancer.Rd ├── exclude_vars_noncoding.Rd ├── figures │ └── logo.png ├── generate_cpsr_report.Rd ├── get_insilico_prediction_statistics.Rd ├── get_max_rows_pr_datatable.Rd ├── load_germline_snv_indel.Rd ├── plot_summary_statistics.Rd ├── plot_virtual_panels.Rd ├── report_color.Rd ├── retrieve_pgx_calls.Rd ├── retrieve_secondary_calls.Rd ├── tidyeval.Rd └── write_cpsr_output.Rd ├── pkgdown ├── _pkgdown.yml ├── assets │ ├── cpsr_superpanel_2024_05.xlsx │ ├── cpsr_superpanel_2025_03.xlsx │ └── img │ │ ├── cpsr_classification.pdf │ │ ├── cpsr_classification.png │ │ ├── cpsr_classification.pptx │ │ ├── cpsr_sc.png │ │ └── cpsr_views.png ├── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico └── index.md └── vignettes ├── .gitignore ├── CHANGELOG.Rmd ├── annotation_resources.Rmd ├── input.Rmd ├── installation.Rmd ├── output.Rmd ├── running.Rmd ├── variant_classification.Rmd └── virtual_panels.Rmd /.Rbuildignore: 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