2335669ca4b3580df846da492b73c583 *DESCRIPTION
19e45a8c2f27e05253fa454118fee752 *LICENSE
e00aa78d6da3eaa445e58066c003127f *NAMESPACE
d4fe51a95c3285f29aaacfed6ed7d2fe *NEWS
b3e64fda2094468187f05a6134e58584 *R/CancerDetector.R
dca14fde6cf919e7fc5994912a6e210e *R/GenerateFragMeth.R
1bf662e29f564123e3897d9b22905778 *R/GenerateMarkerParam.R
0661ad3b246fb8cb08bcf25368617db1 *R/MergeCpGs.R
e86b8dcfa30dc4307a32a0a419fd3f0e *R/MergePEReads.R
659a538be3755710b47b10f59de655b6 *R/PlotFractionPie.R
30220dd741758e1860424da2a1a6e957 *R/RcppExports.R
67b1191663ebf66c17141b8b2a45747a *R/basilisk.R
5b892be79f89503dc20799a5144cde24 *R/cfDeconvolve.R
1e8538ec99bac9c96ab75a602b5e0915 *R/cfSort.R
2f3fa1a1beefee66bbb2b14e780b2d79 *R/cfTools-package.R
8768ff81ff163ae185a19ca6c8682ca1 *R/cfTools.R
2bc73dd61456233ecf3ce866f007b58c *R/data-CancerDetector.markers.R
b5c9e80c4c599a7e2ec469dcf2acec11 *R/data-CancerDetector.reads.R
5946c134cfd45f50fd25fbb07fc57736 *R/data-CpG_OB_demo.R
0d05a45988b771d53b1807b90f1363cb *R/data-CpG_OT_demo.R
39fdb1f4add81f5bb0e974a9273343b9 *R/data-beta_matrix.R
cc26e88608a1daac63659534cc242887 *R/data-cfDeconvolve.markers.R
54f7e9c66c6f269a773993f815e85266 *R/data-cfDeconvolve.reads.R
ee41ba98ea5e60205f2f03140744bf8a *R/data-cfsort_markers.R
eed09b9f38d83fa457870fa230036dc1 *R/data-cfsort_reads.R
f266613f14846e09c1d42401cae4caa6 *R/data-demo.fragment_level.meth.bed.R
b98b1b1346da8062a54659c698938cd6 *R/data-demo.refo_frag.bed.R
885eceac53d0280a67322176283ac109 *R/data-demo.refo_meth.bed.R
3c200d2e72f21f56dcf8cebedf640e8d *R/data-demo.sorted.bed.R
18eb240bfc7558920fcd97047fa56b98 *R/data-markers.bed.R
4e12fb6d7db3a19ce79bddbc9ed5b6d1 *R/data-markers_index.R
80533a0e06a5c407f6cbb47d9e0c6e55 *R/data-sample_type.R
9deaa657ebaf1e18eb2bf99771bba008 *README.md
4d65b9e85040c7dd0a4c142b6e88db45 *build/vignette.rds
357dd961172bf0191dac7d051404333f *configure
3ac2a0c78b45a3a0204268ad4ef4796a *configure.win
c3db69b2e2f98497275ecd006f4645bd *data/CancerDetector.markers.txt.gz
86b44efd624cfb1c9214d41c9d51a983 *data/CancerDetector.reads.txt.gz
5005d3b565af1473d0ff84064f051234 *data/CpG_OB_demo.txt.gz
71702d695a7c7473773548cfd2837213 *data/CpG_OT_demo.txt.gz
13700d8d28126b551c1fad89dc0fa493 *data/beta_matrix.txt.gz
4eb192e1314b90b71acce178d9216155 *data/cfDeconvolve.markers.txt.gz
b76aeb1107d85e9ce0ca314bca057af3 *data/cfDeconvolve.reads.txt.gz
09809721bf2da701026a73f67b83604d *data/cfsort_markers.txt.gz
a2a088c08a944ce65820cf39526cd4e4 *data/cfsort_reads.txt.gz
fa42e295ff8ad0ecb2540683b368d905 *data/demo.fragment_level.meth.bed.txt.gz
bb131a69e22e0cd35d908fdb1399c8ec *data/demo.refo_frag.bed.txt.gz
a16688e7649d5ee80b4a64b2317e2b61 *data/demo.refo_meth.bed.txt.gz
fd0ca366783d4d49c725cc64aac76c32 *data/demo.sorted.bed.txt.gz
f2b8e133a578ec38ab3e6e70cb9a0f6a *data/marker_index.txt.gz
1124ab6ecb9ccb8c09c8572ef9a404c7 *data/markers.bed.txt.gz
0bf28c08bbcf29f0b874b5677d6d5e05 *data/sample_type.txt.gz
06693767ecc8f4fe91af6f16e9d93067 *inst/doc/cfTools-vignette.R
f17efa5d8e7ccae0436d2807acc09208 *inst/doc/cfTools-vignette.Rmd
f6ef7a72b298723a8828ad45d442df9a *inst/doc/cfTools-vignette.html
9b012948f51634d4adddea9490303c1a *inst/python/CalcReadLikelihood.py
43b35207a15387aff6b7a411f33507be *inst/python/CancerDetector.py
86cb542c91eb36c67203ecad9ae3b5ac *inst/python/__pycache__/library_utils.cpython-38.pyc
fbfebb2dcfb71e9c37d44be86400a9a0 *inst/python/__pycache__/utils_analyze_data_mat.cpython-38.pyc
fe87e486b1f4465e2eb893ea6972e111 *inst/python/__pycache__/utils_analyze_markers_data.cpython-38.pyc
5a42ecb133e3813646b65e02739a73b9 *inst/python/collapse_CpG.py
e9432845051b73e7678398e99ccdaa07 *inst/python/collapse_bed_file_strand_correct.py
e2ce2964ed1f2d7beeafe78a57a30553 *inst/python/convert_binary_meth_to_alpha_value_distribution.py
4f15b9c7ea1d2f2cc3d665d77f065fab *inst/python/data_prep.for_test_only.py
8c96bf0cfb1e49237c510e528f33eebe *inst/python/generate_data_matrix_by_alpha_value_and_markers.py
b600f06d2c13d60f18403d50cbdff8a3 *inst/python/library_utils.py
a973809b01850e9d3e6fae08f7cca578 *inst/python/model_pred.py
83293a34e15ab4b6c46c27f17adc579c *inst/python/norm_params.npy
a1e8f05c3de3eeda664445922013c294 *inst/python/normalize_local_read_depth_and_cluster_markers.py
7f53fefceb0b0612149518b99c27211a *inst/python/utils_analyze_data_mat.py
c01ab8db5ccf4e3d27ac05d07a58789f *inst/python/utils_analyze_markers_data.py
ff3c72e87c5f5a410dc9f81532ada09c *man/CancerDetector.Rd
48c8e92842136354e9fbb619fd9f8f59 *man/CancerDetector.markers.Rd
7be1cec36615431a0fc96ef2412464c5 *man/CancerDetector.reads.Rd
3c5b983195f410b3953f6605de9889a3 *man/CpG_OB_demo.Rd
6b40a62e6b6d184aab20d6f03f1547dc *man/CpG_OT_demo.Rd
3ad6b4ee621f087490360a5592865dd0 *man/GenerateFragMeth.Rd
cd00d6d5d878a87c38e4b493cabc7489 *man/GenerateMarkerParam.Rd
1ef6c406eec8aa01bc58294cd1d5f0b2 *man/MergeCpGs.Rd
8c1a46f07307d18c3686def13d5e14be *man/MergePEReads.Rd
4f7c2d5749643d11163e4a803d7a9d16 *man/PlotFractionPie.Rd
b9bb888791d086a2de64fa2abfdbb5b9 *man/beta_matrix.Rd
1435c0ca07fee2b449f5b794b36c292a *man/cfDeconvolve.Rd
2baa07ec04fe24eff6049d53ca0b3750 *man/cfDeconvolve.markers.Rd
2f611e006bdb4994b45691d25c8a48ef *man/cfDeconvolve.reads.Rd
750b2d31e1822d52ceb1ba237e303c16 *man/cfSort.Rd
b4206f11a2844e52d92fb1bf9156e674 *man/cfTools.Rd
b42d8f22bd0e43fba22ee547a062a686 *man/cfsort_markers.Rd
57a76ba4cb20399cfd5e7a7be4afdf70 *man/cfsort_reads.Rd
b3d9986e3551f9b79ac8198dd85305e7 *man/demo.fragment_level.meth.bed.Rd
b3046e6fb22d74ed034c4d5d80da5fed *man/demo.refo_frag.bed.Rd
966c36795bfc3b4243d9af96d71a1618 *man/demo.refo_meth.bed.Rd
909d015947168b4d6a115414e9d61206 *man/demo.sorted.bed.Rd
9b6aeac2b57c84c6181114ee2f1d96da *man/marker_index.Rd
64184c21de79db382415ae1167de8ac2 *man/markers.bed.Rd
11f1d614a8a0ffc0b87ca2daea1b132c *man/sample_type.Rd
7fa019917c543ef2b95222238b235b25 *src/RcppExports.cpp
17015ddb0fddab98ef1dcae79383fc46 *src/data_types.cpp
44f94b0ad3c48c7db94182c4830c7bc4 *src/data_types.h
56ba3a06744ca359f820a5ecbe92747e *src/matrix.cpp
ec73f731e2f7c56ad8db62586e9e5bbd *src/matrix.h
d8f37051a83482c6ce788e0e64c927dd *src/my_getopt.cpp
9a3668430cf5bf3b99074a219f248889 *src/my_getopt.h
006c16a76b52a2622e925d78ecd2d9bc *src/read_deconvolution.cpp
5bfd42f249b766d93b9fee32860eea63 *src/template_utils.cpp
263249db8d502f37794b3edd9a203e8f *src/utils.cpp
b802580c2e253bddc9e7419c3739efbe *src/utils.h
07917436598ed726ce6a7587133f7421 *tests/testthat.R
a45fa0b0aeaf90525b0b5ab9df5fa7cb *tests/testthat/test-CancerDetector.R
a24391b91f41887e0f1f66c384c95dcb *tests/testthat/test-MergeCpGs.R
8a4737947aae4b575e1fca4035d474bb *tests/testthat/test-MergePEReads.R
04059d38becc429d6826a7e1575b75e8 *tests/testthat/test-PlotFractionPie.R
ac0839a20567ee868e13b6adf9ad10d6 *tests/testthat/test-cfDeconvolve.R
36f0b0b6eb47c6926d248c6daa9998ae *tests/testthat/test-cfSort.R
f17efa5d8e7ccae0436d2807acc09208 *vignettes/cfTools-vignette.Rmd
446c3c02124079982ed7610a04429a3e *workflow.png
