bf8feb6149aa8ae2381f75c516cc74dd *DESCRIPTION
b6f7a7af6fedb46ce076cf9b97faf1ae *LICENSE
f39d0b920d8972ff66ed8774ad40c815 *NAMESPACE
5d6cd731c142860ee9785d8d93a29186 *R/analyze_fragmentation.R
b215aacbbdada98a68883e3f6404f298 *R/bin_fragment_size.R
2be55634ba398f902682a2f8e91288a5 *R/create_background_panel.R
2ca100792b5c72703c01120d37c6f5a5 *R/create_background_panel_instance.R
7ad8c673f7baa8c2076f5e95b903037e *R/create_black_list.R
d40f347dbead627f5f69c0765d86828a *R/data.R
7641d94a6008f4b759fdcddbf07f2eda *R/extract_trinucleotide_context.R
0d173cd1a53f83f07bdf6e3910aad750 *R/filter_mutations.R
b50c60b9d7c9dee83898520f45140cca *R/get_background_rate.R
5a3563e72689950299d54939a784add0 *R/get_bam_SM.R
d3e3665895824a9ca497d459c25d9a10 *R/get_bam_chr.R
4d62106f90c0fd90a37d08b2562ae59e *R/get_fragment_size.R
91b75a011f3c7aba2e5d3c3256f4bf4c *R/get_hist_bins.R
2d152a6914e6090ebf6a69adc45d7e92 *R/get_mutation_read_names.R
fe5901a9b9566ab6048f5b9751601937 *R/get_mutations_fragment_size.R
16d3000dbeb895ccf9542ea2b180e28e *R/get_mutations_read_counts.R
3aec16b538e6c99f9ef5bc208e4590ae *R/get_mutations_read_names.R
a9b0c569c89622934b60580eec7bb58d *R/get_read_counts.R
23669f5fc7c76c44c75008e7596c0749 *R/merge_mutations_in_phase.R
fe14b3186fbed38d89be15dfd5f4b37b *R/positivity_test.R
f820a76b927995a798dfa495d8bc00c4 *R/simulator.R
7957f7898688e9d101ecfd757d4b69ad *R/summarize_fragment_size.R
c2437b04ab4b451c03778a311cd2ac00 *R/test_ctDNA.R
5b71472646fc7d6f9541a784e7868c3c *R/vcf_to_mutations_df.R
4f067b51cb9672daf29751535d7b7a02 *R/verify_tag.R
3e5d263c847e6e66048757434d262018 *README.md
d361637e9b3fb89946806a8697ced507 *build/vignette.rds
5a7a69c1a2d712e24ef17e2769e74c99 *data/mutations.rda
cfb7c568cbc5f987d920002c9abc22ec *data/targets.rda
c4a317c335cf4784b2a6f4ba04996504 *inst/CITATION
3f2946ee5e57bbe3fce1c6cb38ee7081 *inst/doc/ctDNAtools.R
581b3c9aca6a538aeab9d12cc5c59eb5 *inst/doc/ctDNAtools.Rmd
17ce5bb4790b5d9a27936d153d1ca29e *inst/doc/ctDNAtools.html
42969473d264313c0f203afb5ef4af2d *inst/extdata/N1.bai
50322e1778ec8c77151d35ceb55120a8 *inst/extdata/N1.bam
8deb27c0b548b6b4031901483a77e6fa *inst/extdata/N2.bai
57ffd3e8b28797c6664e69693a12299d *inst/extdata/N2.bam
665e1f1655e3c6316fcb03a7ad5a33ee *inst/extdata/N3.bai
9695bc43a0fe72ec363bd628d78667a9 *inst/extdata/N3.bam
0c610c80551af6e3c84f6ef4d1f5be66 *inst/extdata/T1.bai
e00a82e540860243d69f59b40de94573 *inst/extdata/T1.bam
51848576fafd87dcd743fc8299555d1b *inst/extdata/T2.bai
0239256e38dafcd10645db1f32e26fe0 *inst/extdata/T2.bam
a195215103bbb9e09c1769061eddf13d *man/analyze_fragmentation.Rd
1ef28d16fc3ef749e906eeb8e6eb966e *man/bin_fragment_size.Rd
a524c98a654442121630b4b82d9b6074 *man/compare_simulated_observed.Rd
dcf8feca7d36594fab55c402d2318500 *man/create_background_panel.Rd
ace2b0bc02b276bce30ffd8bf6570075 *man/create_background_panel_instance.Rd
8a9ef3d91692617b4f2f7861e315411f *man/create_black_list.Rd
c2dc04127c0ad98ea6c9688203c5261c *man/extract_trinucleotide_context.Rd
ef6c62a836b3db709e900047a946911d *man/figures/ctDNAtools_overview.png
d0b50e8118649a1346eaa8cc17cd3530 *man/figures/logo.png
a3e10aa1803c6c03bd362472f958cfaf *man/filter_mutations.Rd
f259f32da4785fa6d27efb8c3b9382b1 *man/get_background_rate.Rd
8d8e44bc29429e5912ded1c173042e0b *man/get_bam_SM.Rd
775f05b9fa425f819fa4fe7be81c328c *man/get_bam_chr.Rd
924283b83963278b4107717b46d423fa *man/get_fragment_size.Rd
8598b50e60c8355d1206aed2c0a8f737 *man/get_hist_bins.Rd
5372623914c2584940a0b0e0276af609 *man/get_mutation_read_names.Rd
0c250c09ad51e72f0fcc6bceb2dcd4fb *man/get_mutations_fragment_size.Rd
a56ae0e132653c0ba81abf29c8470863 *man/get_mutations_read_counts.Rd
8f373e82c153aa436dc08dc46296f57a *man/get_mutations_read_names.Rd
badd0f6ecbd29b66bbea38a14296dd89 *man/get_read_counts.Rd
e0d52d9d21d10e4fd66722c691aa636e *man/merge_mutations_in_phase.Rd
5de4234f0d1f6d924d5921a02103b1c0 *man/mutations.Rd
f21c6bad7be96001ab623da410bd55dd *man/positivity_test.Rd
c1a52962c492988acca9b7f452092726 *man/simulator.Rd
4798d8700e0d48f34d34f0b196a9efe5 *man/summarize_fragment_size.Rd
d17f7bd77791b1cde92e724bc1dc5d7a *man/targets.Rd
787bca696f55c70c066c9869db9540bc *man/test_ctDNA.Rd
18112d48f686a0bb07de681048c9894c *man/vcf_to_mutations_df.Rd
9b5e1ff730c10d41c9b6da98cac3c696 *man/verify_tag.Rd
050dd59ba8abe4a794ceabd96c0acbb8 *tests/testthat.R
b88152e1e560cd24c9f446ee80bb2fcc *tests/testthat/test-ctDNAtest.R
72c96bf88bf20881394e85b88cd9102c *tests/testthat/test-fragment_size.R
793a7f76f8070e496fa2f1be84f715b5 *vignettes/bibliography.bib
581b3c9aca6a538aeab9d12cc5c59eb5 *vignettes/ctDNAtools.Rmd
