0f22115f71f5d09b3053a3c0b2d0441c *DESCRIPTION
986b4e8fc095c7687d77f9cb702b2114 *NAMESPACE
aaf82602abb1da34eec7087c20b23a76 *R/calculate_CES_score.R
d47929efdb23199593f76f8c2344414b *R/call_cnv.R
9b20c67bcdab14304a5d8f872172fea3 *R/create_PoN.R
3ac9e3c45defa2e44bbbf49949efd437 *R/get_fragment_profile.R
cc13efb0e261031b19bed0e15abfe4ca *R/get_solution_table.R
fdbd35d8558de85039e72b8af11facce *R/get_zscore_profile.R
5e6ec3dca3e6d4d1bf8105eb80b416a2 *R/plot_cnv_solution.R
f134c149be95fce29c6fc15b6b2af2e0 *R/plot_distance_matrix.R
3bc72a58c05729c08f9c671bae383449 *R/plot_fragment_dist.R
ebe7225d9ab257fede4afd18e303c91d *R/plot_sl_ratio.R
8e77d806477e56bd026fcb0b4a95be34 *R/plot_transformed_sl.R
06e1c5748cba3aa63a5deb2e77a02fb1 *R/read_bamfile.R
eeacaeb4a90bedb720835645cc492f1b *R/segmentByPSCB.R
fb66204dd11e6e9ddc97b6396a7b97cc *R/utils-pipe.R
c5f53e325580beed7ea5bf2761c645c5 *R/utils.R
ebaf5d2d569b319742cd1c253f87a03f *README.md
abf837be47f152e710128a0ad97a07d7 *build/partial.rdb
c7ff435e36ea391012904f0dbef3e28c *build/vignette.rds
c8a3a2bc8265ac8a0d5a9396f3ee8318 *inst/NEWS
af9a23d25664d9defeabe78f91f190a9 *inst/doc/cfdnakit-vignette.R
5bbd26e34d195ceea64a8598fa67a162 *inst/doc/cfdnakit-vignette.Rmd
25c44740bef4fe683b62fe97cb0b54f1 *inst/doc/cfdnakit-vignette.html
c37e3ef331d132f357b15621919e1d3a *inst/extdata/AnnotationDataFrame_from_QDNAseq_hg19_1000k.rds
7b404f594126dab1646a458082ad90f2 *inst/extdata/AnnotationDataFrame_from_QDNAseq_hg38_1000k.rds
f9c8f0d9671c9e1695ba47b7b7aae06e *inst/extdata/BH01_CHR15.SampleBam.rds
7b788f68a56e99c8edad5b513e858200 *inst/extdata/ex.PoN.rds
8a8ac615b64c262b49c3ad1e141a9c1b *inst/extdata/ex.healthy1.rds
f519d94001b36ba216cd9257b70dbdc3 *inst/extdata/ex.healthy2.rds
da2b958e2b0e564797bea23f28eb4c9d *inst/extdata/ex.plasma.bam
3166601196861ce439ac0959cb9e668b *inst/extdata/example_patientcfDNA_SampleBam.RDS
a3769558e2089816fd52f1c0fc6c2b9e *inst/extdata/example_patientcfDNA_SampleFragment.RDS
7008c778f9c5ace2976cb96a0f0c3f3e *inst/extdata/hg19_centromere.tsv.gz
c5fbefb48ac96af9c85bdda0b6cc224d *inst/extdata/hg19_chrTotalLength.tsv
cd6ad3241298af5e4d5aa3948a6c54f0 *inst/extdata/hg38_chrTotalLength.tsv
e56704d95ec846944e736400e3e05ec9 *inst/extdata/wgEncodeDacMapabilityConsensusExcludable.bed_GRCh37.gz
ffbf9676fae2bf75dd486bd2a6981b2f *inst/script/DescriptionOfExtdata.md
a7fcff769eff7f65112b9ffe44d5b57c *inst/script/extractFragmentProfile.R
56e2ec47e1796a4cd045b6e707ca56a5 *inst/script/run_cfdnakit.R
c664a4f357e7fb8f2b27aeeb07554e6a *man/GRCh2UCSCGRanges.Rd
254bc4ac1bb8572eae3effac2ca59b18 *man/UCSC2GRChSampleBam.Rd
5b4cca3f8601f52ee2be9b4fe1c42114 *man/calculate_CES_score.Rd
ffefd4a22d4075d04537b567a3b274e1 *man/call_cnv.Rd
c9839b31b558b0af89235a2c5fe4416a *man/cfdnakit-package.Rd
980b2cea97dbc597f2e0f3b369507345 *man/create_PoN.Rd
05bc201c2cbf0420acfa931d9b6cac23 *man/create_blacklist_gr.Rd
4daaeffab235fd1a49f63b2136c5bd01 *man/extract_insert_size.Rd
1a9352c30cb1eda4945d4545dd0471af *man/filter_read_on_blacklist.Rd
17f97a8eb59bbf622f7178b0d4c095fa *man/fragment_dist.Rd
e64e97e4a6f96ac1c345ea838a86b3f0 *man/get_fragment_profile.Rd
0e0049186c1d087e140747a2470720bf *man/get_segment_bysolution.Rd
e8a7543e1581587a22f33a57127e525d *man/get_solution_table.Rd
412a614f92d5c13f3fdf4d340345a3c2 *man/get_zscore_profile.Rd
e9c5d8527396f889dfa63dc360971b98 *man/if_exist_baifile.Rd
d1a147e2bac06985feaf013cff376d35 *man/if_ucsc_chrformat.Rd
6b67b55aff8b1cc726886c56778326be *man/make_density_table.Rd
8e99733307d010f8ee1e658f3deff4d5 *man/overlap_bin_with_segment.Rd
cb53cf15b7420f44d43678a24bbdbe6a *man/pipe.Rd
43888d54220b3fb51a1d2139961a647b *man/plot_cnv_solution.Rd
96c12955bb42792e4fc6f0df700904fc *man/plot_distance_matrix.Rd
3022e26e897496242db80ebbefededfd *man/plot_fragment_dist.Rd
c95bf395d01f4bc85bcb8db6338d4de8 *man/plot_sl_ratio.Rd
327c46185b4d98c16fbd2343768c7dab *man/plot_transformed_sl.Rd
929d3e6a238f2b32274f0a732483f271 *man/read_PoN_files.Rd
e5624033d408f14be988b32a2f08c3b8 *man/read_bamfile.Rd
03d91b0fb522cac23add54622b3a812d *man/segmentByPSCB.Rd
b847d8d43d784616af832442876a60e4 *man/test_isize_KolmogorovSmirnov.Rd
caadfd86ff4cf67ba804421de0001f1c *man/util.bias_correct.Rd
4c1694d73cbb351081ac465e22970f56 *man/zscore_transform.Rd
5bbd26e34d195ceea64a8598fa67a162 *vignettes/cfdnakit-vignette.Rmd
