bc5ef876ceb6d96a87f9f312ec0f2776 *DESCRIPTION
bce7cc972e1074ba19eb5baf90ac73f9 *LICENSE
276468d01117975979342e1853335dba *NAMESPACE
2e4d2d4084dfaa51122352433e0255a1 *NEWS.md
1cc56cad3655b2693e8e3c02cf31d2ea *R/CN-mutex-classification-methed.R
6649933011f597e7eb4b04178e6d365c *R/RcppExports.R
a021446c9255ce9a0473e96e59a7081c *R/add_h_arrow.R
93d954e979afc8f890b93226631fa32b *R/add_labels.R
7856acdf24fb99edbea208c73f75f2ef *R/assert.R
c5b6e0f9fde0a827b69dda8a1c1eb5ee *R/bayesianNMF.R
1cc6ec981953310923ffd85153fd42cc *R/best_practice.R
22d58ba7418832802ffbae25aaed775b *R/best_practice_helper.R
1ac1e2073802ed549b29016d8fe39962 *R/class.R
d9c3a4928eba3517f96ea19f58263afd *R/cosine.R
b0f0bdc50415b515bd624fed6df189e8 *R/data.R
d6d7fbfe9f2e87ffd24b381174d30370 *R/enrich_component_strand_bias.R
f0ae2e6bbf2a931e741b12ddcebc4bc4 *R/find_enriched_signature.R
42ecd934e435f98798441b85a39ef473 *R/generate_matrices.R
2dbf5c4ed20439d0f4ea0e05e8454888 *R/get.R
477156ad5eb1305dbc10c019e8b6a56d *R/get_adj_p.R
3c703dc33a2a655d53c9db7906018395 *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
d542ef2704728f67e12cf16f375cc5d9 *R/get_groups.R
e068247415b1e641482e35bca7c17965 *R/get_reconstructed_similarity.R
12fc15ecbb8bbbffefba880393bfd3fc *R/get_shannon_diversity_index.R
378947786682d2fa608de794ec483bbb *R/get_sig_cancer_type_index.R
8f17178d31eabb6af06c63bc8fd8cf27 *R/get_sig_db.R
95daae8c5a86e471b709bafaad8ca12c *R/get_sig_exposure.R
f5f3f137cbc7eb7872b3ebd4dbb50a06 *R/get_sig_feature_association.R
6ddcae98cbf4f860821777b7eea0616f *R/get_sig_optimal_exposure.R
ad90d2867117a5b64e0911c22b886fa9 *R/get_sig_similarity.R
da519d7124dec6c41f7cea4bb8b6d5ae *R/get_sv.R
74389d6ee586b35d82ae21a837be1b06 *R/get_tidy_association.R
405a91f5b2d5a75da677662dadff59b2 *R/get_tidy_parameter.R
7695bb2a14454d65323c8ca57deb23f7 *R/globalVariables.R
9f883e4ba0ed52a1de631f2a2f7558d6 *R/group_enrichment.R
d530f860a17ac6939ea929f6eaf79840 *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
ca87cf5d8baa2b0b88add18cebe1b0e9 *R/helper_fit_cn_components.R
b1ef4ac184d9f6c72eca5c7db49402a1 *R/helper_join_segments.R
df1a91adf8633252d2be0404dbd0d315 *R/helper_normalize_by_feature.R
86946ad5f4fd0f1d8e1f3955fa5a9eed *R/helper_scale_nmf_matrix.R
dd6aa03b11d5f642f4d06f72272a1bd5 *R/helper_sort_signature.R
c60ac83eddba3a3f5902b9cc32cec0cf *R/output.R
0b8a259faf4e9a335f5cd1ab3a02de50 *R/read_copynumber.R
e0c8c385e94a7cf4b265a00fdfa68d29 *R/read_copynumber_seqz.R
b2fb60215f5150002b32e696bc54c5c5 *R/read_maf.R
0b9642e723275374a5842cc21f86f0ef *R/read_vcf.R
74373e495a8ee19ed0c853b16f393f63 *R/same_size_clustering.R
4ee708725d1117ed04b8c7f126dfe51e *R/scoring.R
b86d5bdbbe141422ceae769c64046856 *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
872c5ecd530b99f65767a51a6488345d *R/show_cn_group_profile.R
d42c96027bebd31cef987fdfc772306a *R/show_cn_profile.R
664e23a9aea0ef6726a72e02c6657fd6 *R/show_cor.R
ca363092f51197a839e30e9bdf0cb378 *R/show_cosmic_signature.R
244d48a78cbc535df4141bc8d9a2c4bd *R/show_cosmic_signature_profile.R
7e6998a7d0f7d7509b7a19186724e8ce *R/show_group_comparison.R
8829963804e5c4a87fe7fe3048c7747f *R/show_group_distribution.R
4bb9670c23454eb997f1f69cdf067f5a *R/show_group_enrichment.R
49409943618a850a6a4d1fb015ae5071 *R/show_group_mapping.R
90e5127f39decf4eef841bf0479bf171 *R/show_groups.R
68ebb352c5ef0776707cd7d2a2d25a5f *R/show_sig_bootstrap.R
021f1954f33d34ca4d6abd0af5dc90c3 *R/show_sig_consensusmap.R
a7dfa74272a96a9ec51c7014fcf33f1d *R/show_sig_exposure.R
d539dc586046fd8d361e6c104fda44b2 *R/show_sig_feature_corrplot.R
29d1692d7ae9a0860f4648e654196b44 *R/show_sig_fit.R
5db4a0b76da95274e7b445b8f14e8f58 *R/show_sig_number_survey.R
1a7b35f4c98a090a1309038d78d149b2 *R/show_sig_number_survey2.R
7f9e92a94e9b355838647f0b211bef65 *R/show_sig_profile.R
fa04c7abc967486f2365637344e3fd1f *R/show_sig_profile_heatmap.R
1dfb122a2e7544abaaf5526436e984dc *R/show_sig_profile_loop.R
087a5b211e9dbf037630dad4731015cc *R/sig_auto_extract.R
29656bd696c0c71bf8a122fc897c3fea *R/sig_convert.R
fb7482b246747335d335c97fdc791049 *R/sig_estimate.R
1f75822ca24caf35a4b983bdad0712e2 *R/sig_extract.R
7cf509d2984a4903ad1c65400747e1a0 *R/sig_fit.R
fd86760de4c8785d9e785ad7f531f390 *R/sig_fit_bootstrap.R
7e28c7eddf162eee1197bcc93918def1 *R/sig_fit_bootstrap_batch.R
4a548f68666b074233e4a7369bcdd81e *R/sig_tally.R
69977e14e4e01ce67fd4720b9f1a6d55 *R/sigflow.R
47ab9a23b5a5592592eb25fa51870e6a *R/sigminer.R
5881b8f084c799b10dc4a266c5b66f15 *R/signature_obj_operation.R
6cbe55d7b5d30cfae899a101894e9bf2 *R/sigprofiler.R
af72c2562bb30399d98eb425c5144082 *R/simulation.R
1c96f39fd3894b834644a48ea9ff4de8 *R/transform_seg_table.R
65cef5e0674056f6fc07dd2b3ca85c13 *R/utils-pipe.R
0be6c3cee3a2d2096131c21e8491c40a *R/utils-tidy-eval.R
879fbcdf2d8feef2cb1165978d3a7ee6 *R/utils.R
94d92ee75d8c94ae1ce91d0a6977c4c4 *R/utils_mem.R
e3151b0efa33dd672d14763cf803e147 *R/zzz.R
310f354402424dfaeaf46e31ed269121 *README.md
2212460d2e52e483fbc13daed78c324c *build/partial.rdb
56e5d76e4143496b465088de5bdc76bd *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
1db50f00b962030f1384395d32136963 *data/simulated_catalogs.rda
55ee30572bfe538472eda631f6599ccd *data/transcript.hg19.rda
fbfe48915d4b8e7cd8bbd19ce058c04b *data/transcript.hg38.rda
f016fb5cf892be4352e995fbaa352a86 *data/transcript.mm10.rda
6b41401a596e94d2e5aacac19ddbd456 *inst/CITATION
851a744d4c4fb7fa62245221da4b9457 *inst/doc/sigminer.R
e3319d25b580a2f30dae1c551ee8046c *inst/doc/sigminer.Rmd
b3de5e36e421d17fa71ed8e4453d8cdd *inst/doc/sigminer.html
20ca8938f1d727fed87d19a92c62872d *inst/extdata/CN40-Map.txt
0bd9429341cf2a282088948f6f45fd5b *inst/extdata/CN48-Map.txt
404727e7eb984abd5072fedb049ff06d *inst/extdata/CNS_signatures_USARC.rds
e3e92f94fab3701e369b9d23e8d728d8 *inst/extdata/DBS_signatures.rds
a240c2b1aa5cd64adc65880c29438b37 *inst/extdata/DBS_signatures_list.rds
46e01cf150f46ba35cd89a53ff909241 *inst/extdata/ID_signatures.rds
ddc4f9614e8b43c94bba7ba3c0f8ecdc *inst/extdata/RS_signatures_BRCA560.rds
670ddde512e4d7289b21dbdbe4ece557 *inst/extdata/RS_signatures_Nik_lab.rds
254d8904d666843fd777c04b344b6c46 *inst/extdata/RS_signatures_Nik_lab_Organ.rds
ad26f1415b795e74f3b2c0a0dfbc2f47 *inst/extdata/RS_signatures_USARC.rds
2bc03795aff156b89c2fbf317c79bb42 *inst/extdata/SBS_signatures.rds
4972ea657f11a8710f267c303add6e31 *inst/extdata/SBS_signatures_Nik_lab.rds
b6c4c57e33a266c9f442133f8e218dc8 *inst/extdata/SBS_signatures_Nik_lab_Organ.rds
83cc10fdd3e36499ebff7fba11702ac4 *inst/extdata/SBS_signatures_list.rds
9249ddf35e997ce28b5c2b1e78c5b17d *inst/extdata/TSB_signatures.rds
64b7eb396880bc462a4b23370b265f44 *inst/extdata/asso_data.RData
c00a26667286d596229a6eeaae86ea2f *inst/extdata/cosmic2_record_by_cancer.rds
b869391cdccc84740b0ba4e977ad54ac *inst/extdata/metastatic_tumor.segtab.txt
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
d5b1ff47c6fdbe5620d5dead68dd9d75 *inst/extdata/toy_sv.rds
ef1747d7a289d4aecf0dfa5bfc3cf395 *inst/py/nmf.py
e981190dcb58b5a741734435b3f69fa9 *man/CN.features.Rd
cc8aa6f909b7252f1af727d274d8ea0f *man/CopyNumber-class.Rd
5666b6c86a5e5c48981cf68ce7ba9f17 *man/MAF-class.Rd
1beeecfb378e6add8fb5f1ab12ccdb75 *man/add_h_arrow.Rd
8eceaaf54ba39b934913fa6afc64cd2b *man/add_labels.Rd
bb7aa5e27cebef239535954c16b2437b *man/bp.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
0c3add11a49f50b972f1d3118d919201 *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
7a883224625da57340045fc926a4485c *man/figures/README-unnamed-chunk-1-1.png
43269956fc3ae29bc2cab79c73f9164a *man/figures/README-unnamed-chunk-2-1.png
ea30009877cf084cd280bb006eed882b *man/figures/README-unnamed-chunk-3-1.png
ac0ec48e999087af3c6608d7468b0d46 *man/figures/README-unnamed-chunk-4-1.png
46e13fc2e686dfa8e98efcba5c45b4f5 *man/figures/README-unnamed-chunk-5-1.png
db6e9af2e16dc5d358068e6b71dce8fd *man/figures/README-unnamed-chunk-7-1.png
244c0a4b811b02ffe40a6eb80386becd *man/figures/README-unnamed-chunk-8-1.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
ceecea1ad25e969a2071395d043ed85f *man/get_groups.Rd
3f37a09c1d0a2b604266d7d90cc57f88 *man/get_shannon_diversity_index.Rd
c7cd69b5caeda56266e5c78d6ede3b07 *man/get_sig_cancer_type_index.Rd
e5f16f606e6da64064944f2fd3f53e4d *man/get_sig_db.Rd
6d015c3eb4cc6f51b1019754596ba17a *man/get_sig_exposure.Rd
e259834d1b6f888aa241bee8fd86eefc *man/get_sig_feature_association.Rd
3c836bac66965d411ba9615d222eca4a *man/get_sig_rec_similarity.Rd
a1b613d193583304a61631daae3b7784 *man/get_sig_similarity.Rd
bc9ea372e63c5b0eb3d6b0bf9a875111 *man/get_tidy_association.Rd
93a2529e3c49882c96d2687a07e1249d *man/get_tidy_parameter.Rd
1a1408b04bfc368ace5110a6598811e7 *man/group_enrichment.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
78ea15f09c9845ddfc0d386975464a7b *man/read_copynumber.Rd
f577788b9e99eeee53128dc85a414dee *man/read_copynumber_seqz.Rd
13bcd61266fdf57b8adb63ff204913a7 *man/read_maf.Rd
4027a453e50494f3fa96da977704630f *man/read_sv_as_rs.Rd
9bc24a81a3834b16d066d9b2e1df7720 *man/read_vcf.Rd
b6c58fb6bbb06b571fcddf30161098e4 *man/read_xena_variants.Rd
9dd3bc1e381ee1eda2e21c2c3ac4bfa8 *man/report_bootstrap_p_value.Rd
5296db48e4c4b8a9c5824ce4ae3cabe0 *man/same_size_clustering.Rd
6a4eac5cc9f806524278f5b838f378a3 *man/scoring.Rd
d497e2a88b62c0836989612246cc5f5c *man/show_catalogue.Rd
b66e4d864bbd18457b9210c9dbd7c452 *man/show_cn_circos.Rd
23d7b43914f5245dca1422e65fa3b3dc *man/show_cn_components.Rd
106128827a9f8e3403261007ea998403 *man/show_cn_distribution.Rd
63baf5cf8963bd9475f2a8fbe1f44b06 *man/show_cn_features.Rd
7f884bbda6717cb114a3ce8ea813a913 *man/show_cn_freq_circos.Rd
5ffbd22d7eba0f9f820f32803abd0bec *man/show_cn_group_profile.Rd
fb3aca4e01e9afa4d308d5af7c01e1e9 *man/show_cn_profile.Rd
e49dafd9929fa99f55d1ab3a0b1bcea0 *man/show_cor.Rd
c04a1e0157e1b3ebd6cab183be28b9ce *man/show_cosmic.Rd
88b35f7ea5b3baeca614389b2b0f63ea *man/show_cosmic_sig_profile.Rd
fc8d1793f6d19eca1b49e5e0e80f9f3e *man/show_group_comparison.Rd
3c5fda9633e7c5f19b5ec1383eee81a8 *man/show_group_distribution.Rd
8a85b10b018356f1e449de2a7cf07c74 *man/show_group_enrichment.Rd
4d635e2480c155d9fe881e5e9477ef0e *man/show_group_mapping.Rd
0b221e6ccaad40324900cadbe1c068fd *man/show_groups.Rd
439311252baefc6751743c5e13f60d85 *man/show_sig_bootstrap.Rd
6bb93ff096c95a3ece515fc2a1e6572b *man/show_sig_consensusmap.Rd
699477628a3e0b1a847cd38a215b94af *man/show_sig_exposure.Rd
0d7dba2df72e32ffcc3198752c6618f7 *man/show_sig_feature_corrplot.Rd
6aefba88eeafeb7b6052ba286c33a9fb *man/show_sig_fit.Rd
102ef18df63cb764e6d0a15e845a3bc3 *man/show_sig_number_survey.Rd
6d30887e9f4a7eade82e68582d4f12db *man/show_sig_number_survey2.Rd
dfb15a50356a75100d4a7af975a35a85 *man/show_sig_profile.Rd
b8eeeb886dd35dac6e33de9555cf2343 *man/show_sig_profile_heatmap.Rd
f127c8b5e62660686e247c69ca9d2e23 *man/show_sig_profile_loop.Rd
0e59ef1b691263b2c053663a516443c0 *man/sig_auto_extract.Rd
07bd4379f328f5e72e5b177b8107caaa *man/sig_convert.Rd
ab5b7ecd179957f8e8957b611bd29d00 *man/sig_estimate.Rd
f2405f12bfcb80432672234975d90d3d *man/sig_extract.Rd
3ec305d00c8316b8d9af04ee1e6e5a84 *man/sig_fit.Rd
b50fa4a6aa137f7e10937ff0642cf455 *man/sig_fit_bootstrap.Rd
52337cab28f8d07d0c36344c29b7e166 *man/sig_fit_bootstrap_batch.Rd
3c90742a6846156c0b97815dbf38aaad *man/sig_operation.Rd
0b270ca872ac185375501083e0220c87 *man/sig_tally.Rd
8a3d0c50f050125d0c9789da687e7d60 *man/sigminer.Rd
c8a1609e88a3869010c60ae26f7d29b5 *man/sigprofiler.Rd
e4e54503b4569ed3f965a1ee37a34024 *man/simulated_catalogs.Rd
33b9d70620c26d4e87c1634567a3289c *man/simulation.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
d5313c5d3b9b44bd638df9a9075aa3f3 *man/use_color_style.Rd
2ffdeceda27adce30538a8e35658f3d5 *src/RcppExports.cpp
cc3fb55d2e112805a9a754b5fa6c5202 *src/calc_cosine.cpp
187c742c13e902d2e935a04b38e30cf2 *vignettes/e1.rds
e3319d25b580a2f30dae1c551ee8046c *vignettes/sigminer.Rmd
