23cda9859b31d3997e4325c3fe59b12f *DESCRIPTION
bce7cc972e1074ba19eb5baf90ac73f9 *LICENSE
5bb4ae18f5248a9d2f62f06cff1d5960 *NAMESPACE
2270563733a058f27216b685e805ae41 *NEWS.md
9b1352357c26b8a27a577882e981e59c *R/CN-mutex-classification-methed.R
6649933011f597e7eb4b04178e6d365c *R/RcppExports.R
a021446c9255ce9a0473e96e59a7081c *R/add_h_arrow.R
9f59f662894c18ba2ca0a8fe086d334f *R/add_labels.R
7856acdf24fb99edbea208c73f75f2ef *R/assert.R
c5b6e0f9fde0a827b69dda8a1c1eb5ee *R/bayesianNMF.R
1ac1e2073802ed549b29016d8fe39962 *R/class.R
f89dff052d820044c575f71e57f39118 *R/cosine.R
612fc9f687f6ed2f5c7878ea35316a16 *R/data.R
d6d7fbfe9f2e87ffd24b381174d30370 *R/enrich_component_strand_bias.R
f0ae2e6bbf2a931e741b12ddcebc4bc4 *R/find_enriched_signature.R
e4b0852959fb67fee6f70c343d94d695 *R/generate_matrices.R
3685d5a7432a85f1b88e1fe14b0dc5fe *R/get.R
477156ad5eb1305dbc10c019e8b6a56d *R/get_adj_p.R
af4bd056090396fcf919daf557f9320a *R/get_bayesian_result.R
eb6e4269736c0e90551c67de0727cab6 *R/get_cn_freq_table.R
3ca63279540da3e6dfb12422cc5977b4 *R/get_cn_ploidy.R
11e9794f31ba86ed12434a247505b6b9 *R/get_genome_annotation.R
bd4b9a71e025ae551bde443d9380f647 *R/get_group_comparison.R
1bcee4d8cc2a80eaa30bc434a7e97640 *R/get_groups.R
378947786682d2fa608de794ec483bbb *R/get_sig_cancer_type_index.R
43dd064db6e8d7a7dfa5865aada49013 *R/get_sig_exposure.R
f5f3f137cbc7eb7872b3ebd4dbb50a06 *R/get_sig_feature_association.R
6ddcae98cbf4f860821777b7eea0616f *R/get_sig_optimal_exposure.R
c4bd29ed1628f1a7716cad0181151584 *R/get_sig_similarity.R
74389d6ee586b35d82ae21a837be1b06 *R/get_tidy_association.R
405a91f5b2d5a75da677662dadff59b2 *R/get_tidy_parameter.R
72bfc2ef7826d17334a27977730db505 *R/globalVariables.R
c8a031c777c07f68cf485b43f76861a6 *R/handle_hyper_mutation.R
ec28a696949c90a70d6c36ad6b17f32a *R/hello.R
2af32d0f4257858b51db422a4e057385 *R/helper_calc_sum_of_events.R
94726eb225509e3a902e0751b70e0b0b *R/helper_create_chunks.R
64d4edaab01a9ffad0885639311e705d *R/helper_create_colormap.R
200d26bc634e050442efb8a4ae44418c *R/helper_derive_cn_features.R
fd17bc5f18452df57269e99aa0ddc8c3 *R/helper_fit_cn_components.R
cf3e76310d2f3efc015895861c137507 *R/helper_join_segments.R
df1a91adf8633252d2be0404dbd0d315 *R/helper_normalize_by_feature.R
76e0d449b5eb5bb69ee1cf9a21d22f87 *R/helper_scale_nmf_matrix.R
dd6aa03b11d5f642f4d06f72272a1bd5 *R/helper_sort_signature.R
5b63ecde5d31ffee8c260a0cc1a32e5e *R/output.R
523a42b10be0a475027968eed2a2ff40 *R/read_copynumber.R
e0c8c385e94a7cf4b265a00fdfa68d29 *R/read_copynumber_seqz.R
b2fb60215f5150002b32e696bc54c5c5 *R/read_maf.R
627898828bd522afd93271e1bb4ab97d *R/read_vcf.R
2b21ac9e830649b6af9b54e2731706ad *R/scoring.R
2cad51f826d0753507e24df7068a5fb7 *R/show_catalogue.R
58f7517ba31872c9c1f6c50e93eae73d *R/show_cn_circos.R
587e25c5e76d2c6554d8e3bfa5538f63 *R/show_cn_components.R
c7368d6459389c8950d077a7389e1641 *R/show_cn_distribution.R
4cda8ffe578fb2d7d2d080a4d4d87180 *R/show_cn_features.R
9d8735be6ccc4bf8cd29ccc7eb269203 *R/show_cn_freq_circos.R
37ea033d00a155a67fd81b9c92f51575 *R/show_cn_group_profile.R
d42c96027bebd31cef987fdfc772306a *R/show_cn_profile.R
0468209429344a311fb209781236f5f4 *R/show_cosmic_signatures.R
7e6998a7d0f7d7509b7a19186724e8ce *R/show_group_comparison.R
7cc926937114606f870512bcc9f01be1 *R/show_group_distribution.R
49409943618a850a6a4d1fb015ae5071 *R/show_group_mapping.R
90e5127f39decf4eef841bf0479bf171 *R/show_groups.R
9ed05cc14a163f93747d9320f4c38ceb *R/show_sig_bootstrap.R
021f1954f33d34ca4d6abd0af5dc90c3 *R/show_sig_consensusmap.R
f4fd3db4d0affd930576198d56f25a56 *R/show_sig_exposure.R
6f220fe6a6eec5ed5c917100accf18ec *R/show_sig_feature_corrplot.R
29d1692d7ae9a0860f4648e654196b44 *R/show_sig_fit.R
355e4f4f0fba369bea8ebe75a7c6a3b1 *R/show_sig_number_survey.R
fcc487965fda5d2ab6f2ab8c9ccdca64 *R/show_sig_number_survey2.R
da2c8d23f74630ef9778311a729a4ab5 *R/show_sig_profile.R
fa04c7abc967486f2365637344e3fd1f *R/show_sig_profile_heatmap.R
33d203a717007f800d0681fe4dd7c64a *R/show_sig_profile_loop.R
85043c8c1c400ed87860b0ccf4fca0b3 *R/sig_auto_extract.R
9de6ee42d6cb885aae704bfd3b010e3d *R/sig_convert.R
8341efedec67837263f9da40b1221975 *R/sig_estimate.R
6db121058e354cd036da42fbda91a0e4 *R/sig_extract.R
5ff900469f5e72ebde390e455418611b *R/sig_extract_WTSI.R
d97200d1f6361676f1a6df73f6aabc9e *R/sig_fit.R
6ef55ffcc9a8f536f5eabd216ea0b54a *R/sig_fit_bootstrap.R
356e8172a9aa14e96f0282367390fe10 *R/sig_fit_bootstrap_batch.R
c0cdeb6ea00c0bac7b4becd752e6dddb *R/sig_tally.R
73ee819cf90f97d06f921461bd997389 *R/sigminer.R
a6402b5086befdf3e13934c8d386436a *R/signature_obj_operation.R
a06ba50cc3e39e34f7675edabbea0d8e *R/sigprofiler.R
1c96f39fd3894b834644a48ea9ff4de8 *R/transform_seg_table.R
65cef5e0674056f6fc07dd2b3ca85c13 *R/utils-pipe.R
0be6c3cee3a2d2096131c21e8491c40a *R/utils-tidy-eval.R
28c88c41beb749fd5b5261d95e1371cc *R/utils.R
e3151b0efa33dd672d14763cf803e147 *R/zzz.R
1005b28f5c9bdc6c56f08500870fc3eb *README.md
4ce5d2c1161b8c8d947521dbdea6246f *build/vignette.rds
5ba403d476bdc5dbe1706dfef410219f *data/CN.features.rda
d3d9f942b87249a47f7794facc5e55a5 *data/centromeres.hg19.rda
66bcbac28c945b880bf07f0d3410f143 *data/centromeres.hg38.rda
d908919f8f806d11b833ee223712c941 *data/centromeres.mm10.rda
80787271d57544518853d8c691c8fdb2 *data/chromsize.hg19.rda
8c245814898b43e4c3614d360941a3a2 *data/chromsize.hg38.rda
1ac4c885496ce374ef7c173ec5bc1aa9 *data/chromsize.mm10.rda
6457e159b25b42859dc8daa0cf75daa8 *data/cytobands.hg19.rda
1ff1cb0b5d4626ad8c41c1a3697790d9 *data/cytobands.hg38.rda
ad5975138ada9d881a7ab73c8de43a96 *data/cytobands.mm10.rda
55ee30572bfe538472eda631f6599ccd *data/transcript.hg19.rda
fbfe48915d4b8e7cd8bbd19ce058c04b *data/transcript.hg38.rda
f016fb5cf892be4352e995fbaa352a86 *data/transcript.mm10.rda
6b41401a596e94d2e5aacac19ddbd456 *inst/CITATION
1b3bad354aabae765794d9b6092da766 *inst/doc/sigminer.Rmd
9082304ca901ec26c1c5ebdd3165650d *inst/doc/sigminer.html
ba8e5f70c8dcb0978e0aa6e19e19d61a *inst/extdata/DBS_signatures.rds
f7cc805c481377a768800453a6b4d12b *inst/extdata/ID_signatures.rds
d6adda94e5cb71d62d5f7d4103acdc0e *inst/extdata/TSB_signatures.rds
64b7eb396880bc462a4b23370b265f44 *inst/extdata/asso_data.RData
c00a26667286d596229a6eeaae86ea2f *inst/extdata/cosmic2_record_by_cancer.rds
b47bfdf1ec3fd0c1e833f135e5556d90 *inst/extdata/human_hg19_gene_info.rds
e0299f359cd39937b1db61acdd205bf8 *inst/extdata/human_hg38_gene_info.rds
b869391cdccc84740b0ba4e977ad54ac *inst/extdata/metastatic_tumor.segtab.txt
13e38d1ea22a269ba985ca4e40466ee9 *inst/extdata/mouse_mm10_gene_info.rds
b327bb84fa655c8564d019218f74caed *inst/extdata/signature_record_by_cancer.rds
9d2382bfdd50e3cf21d4fd1127fd3812 *inst/extdata/test1.vcf
ccb4fe81e12091f0ecacff7d11aa104a *inst/extdata/test2.vcf
8da6dc61216fc0ad3fc60aaea24fe5ea *inst/extdata/test3.vcf
9371bc15caa55a2b820c1964363c5937 *inst/extdata/toy_cn.RData
c9ca6a19ce13b210484897c3f728a86e *inst/extdata/toy_cnlist.RData
3f2496c30773f05f63ae17bc59bb3d2a *inst/extdata/toy_copynumber.RData
ecdf12a3455108935d128ef82355cbaf *inst/extdata/toy_copynumber_signature_by_M.RData
f6cee69ecce207493ffdeb68c030f648 *inst/extdata/toy_copynumber_signature_by_W.RData
ff52f83effa801ed4051fde8c95c3eed *inst/extdata/toy_copynumber_tally_M.RData
b8bbfa7d5f33361251fcaf4aeadde39c *inst/extdata/toy_copynumber_tally_W.RData
35cfd32e0fd5e416a575db76b5187ccd *inst/extdata/toy_mutational_signature.RData
9460090d01474dcc34f60936130b8dbd *inst/extdata/toy_segTab.RData
7abab37f353d89b735c9d24a33b32b26 *inst/figures/array2.png
cbeb21d8cdaf2a81c2f516973e312681 *inst/figures/barchart.png
e3d055610565332220419dcb581729c3 *inst/figures/sigminer.png
00ac7f566109bb1096bf7b82cb2aea43 *man/CN.features.Rd
cc8aa6f909b7252f1af727d274d8ea0f *man/CopyNumber-class.Rd
5666b6c86a5e5c48981cf68ce7ba9f17 *man/MAF-class.Rd
1beeecfb378e6add8fb5f1ab12ccdb75 *man/add_h_arrow.Rd
66ebd5d1a3d2aa938d08e23753d2a09f *man/add_labels.Rd
2b48a6d5699763a6224dd0e816e9a6d8 *man/centromeres.hg19.Rd
e830582bc2c22badb7798e66de5e169b *man/centromeres.hg38.Rd
9002db4166b704dab3251dad20ddcce1 *man/centromeres.mm10.Rd
af766686247d6781cbcf0f153f15156b *man/chromsize.hg19.Rd
6f44409230726057fca32db2bd2d05af *man/chromsize.hg38.Rd
9280da4726d7af7d5aa98e5a41121bea *man/chromsize.mm10.Rd
e13544d78c05b1845aeefd933353d090 *man/cosine.Rd
5874c06debdd4bc4d1a16665d7ce644d *man/cytobands.hg19.Rd
c9ed77810ef14255c2992b1d0268b67e *man/cytobands.hg38.Rd
53b8df103e50cb2ce385b9066e595369 *man/cytobands.mm10.Rd
b6031594a1fabbc8c04ae9dee2c6041c *man/enrich_component_strand_bias.Rd
b35c5937f9dc96fccde9538d9a720982 *man/figures/README-unnamed-chunk-1-1.png
2f991961cacdb655e420c51265e14203 *man/figures/README-unnamed-chunk-2-1.png
903cfa495d1f68e18e39fa0397f55383 *man/figures/README-unnamed-chunk-3-1.png
6ac85a40f265189026a90427601dc67b *man/figures/README-unnamed-chunk-4-1.png
b41d6d999994ed44e0d3cad5f8157c5b *man/figures/README-unnamed-chunk-7-1.png
e3d055610565332220419dcb581729c3 *man/figures/logo.png
d1f818154dcdf7d16d46820a45ee99cf *man/get_adj_p.Rd
d271df2afcf99b8d0da15de761fd1c05 *man/get_bayesian_result.Rd
b27b6162dabe25221b3e40b5c750a8b9 *man/get_cn_freq_table.Rd
9cdcd9cb6bef6984d473fee97730cf96 *man/get_cn_ploidy.Rd
99b6db140e35bf59baf85ed5ebbe682c *man/get_genome_annotation.Rd
6eae8411c34e316b88de05582842c1fa *man/get_group_comparison.Rd
867e76a8a22464204df9ac6ec21ad2cf *man/get_groups.Rd
c7cd69b5caeda56266e5c78d6ede3b07 *man/get_sig_cancer_type_index.Rd
b54d35e889ef04daff7d5be8dbffa708 *man/get_sig_db.Rd
9fad9df42c5916db66a917ac1f80693f *man/get_sig_exposure.Rd
e259834d1b6f888aa241bee8fd86eefc *man/get_sig_feature_association.Rd
0b1ea665a644155ea7ec9b0b050f4ecf *man/get_sig_similarity.Rd
bc9ea372e63c5b0eb3d6b0bf9a875111 *man/get_tidy_association.Rd
93a2529e3c49882c96d2687a07e1249d *man/get_tidy_parameter.Rd
298eeaa1ac5a173b3a02d28793994cf5 *man/handle_hyper_mutation.Rd
57106e84fe7e0da75ecca6c9af270d43 *man/hello.Rd
eb20a976276c8c4899c97d3cc695d1cd *man/output_bootstrap.Rd
c23e68cd70ba1129d61d9439b5db86c9 *man/output_fit.Rd
c8b7dc057ec9ad1a3ed8759c0006163b *man/output_sig.Rd
de4f29385e753f9659a9a681a21baef6 *man/output_tally.Rd
4894ca10756199e25f914bfd34f517b0 *man/pipe.Rd
b8f4c8a6359ac4cd46868258d4bd3abe *man/read_copynumber.Rd
f577788b9e99eeee53128dc85a414dee *man/read_copynumber_seqz.Rd
13bcd61266fdf57b8adb63ff204913a7 *man/read_maf.Rd
72d2f09119ce2d512361e40b596d074f *man/read_vcf.Rd
9dd3bc1e381ee1eda2e21c2c3ac4bfa8 *man/report_bootstrap_p_value.Rd
943ecaba1a28458d11e58dcc2647ebee *man/scoring.Rd
3ad5a2f81e7550aae919cf06f90dfb3c *man/show_catalogue.Rd
b66e4d864bbd18457b9210c9dbd7c452 *man/show_cn_circos.Rd
221edecaec1c768c0c228970f3d3524e *man/show_cn_components.Rd
106128827a9f8e3403261007ea998403 *man/show_cn_distribution.Rd
33d004e20bcbcb202032736b7a1f9de9 *man/show_cn_features.Rd
7f884bbda6717cb114a3ce8ea813a913 *man/show_cn_freq_circos.Rd
de825c3488cc130bdc361c121e636758 *man/show_cn_group_profile.Rd
fb3aca4e01e9afa4d308d5af7c01e1e9 *man/show_cn_profile.Rd
6912daf8fe6aebf00d4b3ddcb0fd38d9 *man/show_cosmic_sig_profile.Rd
fc8d1793f6d19eca1b49e5e0e80f9f3e *man/show_group_comparison.Rd
3a1521a27491def7f70c01ce87e2ab09 *man/show_group_distribution.Rd
4d635e2480c155d9fe881e5e9477ef0e *man/show_group_mapping.Rd
0b221e6ccaad40324900cadbe1c068fd *man/show_groups.Rd
f6e08613297e4d93f7aed2d3a2262014 *man/show_sig_bootstrap.Rd
6bb93ff096c95a3ece515fc2a1e6572b *man/show_sig_consensusmap.Rd
7a29d276441ce5947b88f03bfa43bdcd *man/show_sig_exposure.Rd
9386a4d96af7400c2fe8a07a51bac16f *man/show_sig_feature_corrplot.Rd
6aefba88eeafeb7b6052ba286c33a9fb *man/show_sig_fit.Rd
f631965006ecd62f9551b99dd7bb3375 *man/show_sig_number_survey.Rd
d096ebd909daac7d04a771268378b149 *man/show_sig_number_survey2.Rd
e452a20c9a8fb8c5ac04b600af995d87 *man/show_sig_profile.Rd
74037f3e5a35b0ac6486509704720d7a *man/show_sig_profile_heatmap.Rd
c1c3eea5d17525a87380ad605b92eed3 *man/show_sig_profile_loop.Rd
24177679d64b1c322306fe14d437a829 *man/sig_auto_extract.Rd
ca484812829bf0a8045924fc859b570d *man/sig_convert.Rd
d317ad8e993a4ee83dc9bd1b7bcff14b *man/sig_estimate.Rd
00a82590fd8e3ad2242f93dc9f629c08 *man/sig_extract.Rd
deed5634206d283d3d38be4f927f5a5e *man/sig_fit.Rd
a6e186ab64ab498e3d9b514996270dab *man/sig_fit_bootstrap.Rd
f0052e12a40904be598c87ce566b665a *man/sig_fit_bootstrap_batch.Rd
4371e73f1aa57c50030099b18eb36f79 *man/sig_operation.Rd
143ea5f336edce329eff36e144884f81 *man/sig_tally.Rd
f0b5d42beb7336d770d32bca750782bb *man/sigminer.Rd
56abad89c0887d5173dd91d2e51a725a *man/sigprofiler.Rd
3711939410914988afd94ae80f35004c *man/subset.CopyNumber.Rd
75a7f110e0b2bb6e6a1c155f3717e6c1 *man/tidyeval.Rd
f8dea68966828488c2881ad5b9d25538 *man/transcript.hg19.Rd
5909588f536b4afd3937d5982e6f8fe4 *man/transcript.hg38.Rd
206f630235f2bf85dceb84df1b6087c3 *man/transcript.mm10.Rd
06d03cad3602e2d14de43a17713ea275 *man/transform_seg_table.Rd
8a4aa08fb288eb231403aa309d92f7c9 *man/use_color_style.Rd
2ffdeceda27adce30538a8e35658f3d5 *src/RcppExports.cpp
cc3fb55d2e112805a9a754b5fa6c5202 *src/calc_cosine.cpp
1b3bad354aabae765794d9b6092da766 *vignettes/sigminer.Rmd
