├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── analyze_fragmentation.R ├── bin_fragment_size.R ├── create_background_panel.R ├── create_background_panel_instance.R ├── create_black_list.R ├── data.R ├── extract_trinucleotide_context.R ├── filter_mutations.R ├── get_background_rate.R ├── get_bam_SM.R ├── get_bam_chr.R ├── get_fragment_size.R ├── get_hist_bins.R ├── get_mutation_read_names.R ├── get_mutations_fragment_size.R ├── get_mutations_read_counts.R ├── get_mutations_read_names.R ├── get_read_counts.R ├── merge_mutations_in_phase.R ├── positivity_test.R ├── simulator.R ├── summarize_fragment_size.R ├── test_ctDNA.R ├── vcf_to_mutations_df.R └── verify_tag.R ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── cran-comments.md ├── data ├── mutations.rda └── targets.rda ├── inst ├── CITATION └── extdata │ ├── N1.bai │ ├── N1.bam │ ├── N2.bai │ ├── N2.bam │ ├── N3.bai │ ├── N3.bam │ ├── T1.bai │ ├── T1.bam │ ├── T2.bai │ └── T2.bam ├── man ├── analyze_fragmentation.Rd ├── bin_fragment_size.Rd ├── compare_simulated_observed.Rd ├── create_background_panel.Rd ├── create_background_panel_instance.Rd ├── create_black_list.Rd ├── extract_trinucleotide_context.Rd ├── figures │ ├── ctDNAtools_overview.png │ └── logo.png ├── filter_mutations.Rd ├── get_background_rate.Rd ├── get_bam_SM.Rd ├── get_bam_chr.Rd ├── get_fragment_size.Rd ├── get_hist_bins.Rd ├── get_mutation_read_names.Rd ├── get_mutations_fragment_size.Rd ├── get_mutations_read_counts.Rd ├── get_mutations_read_names.Rd ├── get_read_counts.Rd ├── merge_mutations_in_phase.Rd ├── mutations.Rd ├── positivity_test.Rd ├── simulator.Rd ├── summarize_fragment_size.Rd ├── targets.Rd ├── test_ctDNA.Rd ├── vcf_to_mutations_df.Rd └── verify_tag.Rd ├── tests ├── testthat.R └── testthat │ ├── test-ctDNAtest.R │ └── test-fragment_size.R └── vignettes ├── .gitignore ├── bibliography.bib └── ctDNAtools.Rmd /.Rbuildignore: 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