Files in Townsend-Lab-Yale/cancereffectsizeR
Calculate Cancer Effect Size
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/CESAnalysis.R
R/add_variants.R
R/annotate_variants.R
R/assign_group_average_trinuc_rates.R
R/build_RefCDS.R
R/ces_variant.R
R/classes.R
R/compound_variants.R
R/covered_regions_handling.R
R/create_refset.R
R/detect_mnv.R
R/epistasis_objectives.R
R/gene_mutation_rates.R
R/genome_data_handling.R
R/get_TCGA_project_MAF.R
R/imports.R
R/internal_read_maf.R
R/load_maf.R
R/load_sample_data.R
R/make_PathScore_input.R
R/mutation_rate_calc.R
R/mutational_signature_effects.R
R/pairwise_epistasis.R
R/plot_effects.R
R/plot_epistasis.R
R/plot_signature_effects.R
R/preload_maf.R
R/run_deconstructSigs.R
R/run_mutational_patterns.R
R/select_samples.R
R/select_variants.R
R/set_gene_rates.R
R/set_signature_weights.R
R/set_trinuc_rates.R
R/si_uniroot_conf_int.R
R/single_variant_si_objectives.R
R/suggest_cosmic_signatures_to_remove.R
R/sysdata.rda
R/trinuc_mutation_rates.R
R/variant_counts.R
R/variant_id_handling.R
R/vcf_to_maf_table.R
README.md
_pkgdown.yml
data-raw/build_ces.refset.hg19.R
data-raw/build_codon_snvs_to_aa.R
data-raw/build_deconstructSigs_stuff.R
data-raw/generate_cosmic_v3.1_hg19_signature_set.R
data-raw/generate_sysdata.R
data-raw/tutorial/prep_BRCA_met_tgs.R
data-raw/tutorial/prep_TCGA_BRCA_clinical.R
data-raw/tutorial/run_tutorial_data.R
doc/cosmic_cancer_type_note.R
doc/cosmic_cancer_type_note.Rmd
doc/cosmic_cancer_type_note.html
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index.md
inst/CITATION
inst/PathScore/PathScore_CDS_ranges_hg19.rds
inst/PathScore/PathScore_CDS_ranges_hg38.rds
inst/WORDLIST
inst/extdata/COSMIC_SBS_v3-1.txt
inst/extdata/COSMIC_v3.1_signature_metadata.txt
inst/extdata/COSMIC_v3.2_signatures_by_cancer_type.txt
inst/extdata/brca_tcga_clinical_data_via_gdac_cbioportal.tsv
inst/extdata/cosmic_sbs_signature_summary.txt
inst/extdata/trinuc_snv_to_deconstructSigs_ID.txt
inst/tutorial/BRCA_cesa_gene_rates.rds
inst/tutorial/BRCA_cesa_samples.rds
inst/tutorial/BRCA_dndscv_out.rds
inst/tutorial/BRCA_effects_in_top_genes.rds
inst/tutorial/BRCA_epistasis_example.rds
inst/tutorial/BRCA_site_rates_example.rds
inst/tutorial/BRCA_snv_counts.rds
inst/tutorial/LUAD_sig_effects.rds
inst/tutorial/TCGA_BRCA_clinical.txt
inst/tutorial/comp_variant_ep.rds
inst/tutorial/gene_ep_example.rds
inst/tutorial/metastatic_breast_2021_hg38.maf
inst/tutorial/metastatic_breast_2021_license.txt
inst/tutorial/sequential_signif_output.rds
inst/tutorial/top_BRCA_effects.rds
inst/tutorial/top_LUAD_effects.rds
inst/tutorial/variant_ep_example.rds
man/CESAnalysis.Rd
man/CompoundVariantSet.Rd
man/aac_to_snv_ids.Rd
man/add_covered_regions.Rd
man/add_variants.Rd
man/annotate_variants.Rd
man/artifact_account.Rd
man/assign_gr_to_coverage.Rd
man/assign_group_average_trinuc_rates.Rd
man/baseline_mutation_rates.Rd
man/build_RefCDS.Rd
man/calculate_trinuc_rates.Rd
man/ces_epistasis.Rd
man/ces_gene_epistasis.Rd
man/ces_variant.Rd
man/check_for_ref_data.Rd
man/check_sample_overlap.Rd
man/clean_granges_for_cesa.Rd
man/clear_effect_output.Rd
man/clear_epistasis_output.Rd
man/clear_gene_rates.Rd
man/clear_sample_data.Rd
man/clear_trinuc_rates_and_signatures.Rd
man/complete_aac_ids.Rd
man/convert_signature_weights_for_mp.Rd
man/copy_cesa.Rd
man/cosmic_signature_info.Rd
man/create_refset.Rd
man/define_compound_variants.Rd
man/detect_mnv.Rd
man/dot-add_covered_regions.Rd
man/dot-variant_counts.Rd
man/epistasis_results.Rd
man/excluded_maf_records.Rd
man/figures/current_logo.png
man/gene_mutation_rates.Rd
man/get_PathScore_coding_regions.Rd
man/get_TCGA_project_MAF.Rd
man/get_ces_signature_set.Rd
man/get_cesa_bsg.Rd
man/get_dndscv_model_fit.Rd
man/get_gene_rates.Rd
man/get_gr_from_table.Rd
man/get_ref_data.Rd
man/get_refset_dirs.Rd
man/get_sample_info.Rd
man/get_signature_weights.Rd
man/get_trinuc_rates.Rd
man/identify_maf_variants.Rd
man/list_ces_covariates.Rd
man/list_ces_refsets.Rd
man/list_ces_signature_sets.Rd
man/load_cesa.Rd
man/load_maf.Rd
man/load_sample_data.Rd
man/maf_records.Rd
man/make_PathScore_input.Rd
man/mutational_signature_effects.Rd
man/pairwise_epistasis_lik.Rd
man/pairwise_variant_epistasis.Rd
man/plot_effects.Rd
man/plot_epistasis.Rd
man/plot_signature_effects.Rd
man/preload_maf.Rd
man/preload_ref_data.Rd
man/read_in_maf.Rd
man/read_vcf.Rd
man/run_deconstructSigs.Rd
man/run_dndscv.Rd
man/run_mutational_patterns.Rd
man/samples_with.Rd
man/save_cesa.Rd
man/select_samples.Rd
man/select_variants.Rd
man/set_gene_rates.Rd
man/set_refset_dir.Rd
man/set_signature_weights.Rd
man/set_trinuc_rates.Rd
man/snv_results.Rd
man/sort_and_validate_variant_ids.Rd
man/sswm_lik.Rd
man/suggest_cosmic_signature_exclusions.Rd
man/trinuc_mutation_rates.Rd
man/trinuc_snv_counts.Rd
man/univariate_si_conf_ints.Rd
man/update_covered_in.Rd
man/validate_aac_ids.Rd
man/validate_signature_set.Rd
man/validate_snv_ids.Rd
man/variant_counts.Rd
man/vcfs_to_maf_table.Rd
pkgdown/extra.css
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pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
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tests/generate_test_data/generate_brca_test_maf.R
tests/generate_test_data/generate_gene_rate_test_cesa.R
tests/generate_test_data/generate_refcds_test.R
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tests/generate_test_data/generate_trinuc_data.R
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tests/test_data/luad.hg19.maf.txt
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user_guide/cancereffectsizeR_user_guide.Rmd
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vignettes/.gitignore
vignettes/MAF_filtering_tips.Rmd
vignettes/cancereffectsizeR.Rmd
vignettes/cosmic_cancer_type_note.Rmd
vignettes/create_custom_covariates.Rmd
vignettes/custom_refset_instructions.Rmd
