51ad044d1e84c6670d3f9fc010b73d17 *CITATION
d62f86a7c4e3056021781ca63631d25c *DESCRIPTION
1bec231b719d8db0df825d414ef1771d *INDEX
28dad4492fcf2f517fc721fd2834f28b *LICENSE
48e7f46f4c3b3423776cad5a8fcb7c94 *Meta/Rd.rds
1d15b8cd6573641f81c4126b0438e9c2 *Meta/features.rds
c5709b61b1e2d92634c6b8acfbc40181 *Meta/hsearch.rds
7ac6c27f02f83799dca110f2f21f8448 *Meta/links.rds
ec5e573a90e0f61b782a8cd5fd1fc960 *Meta/nsInfo.rds
27e9a5f4a5b461f6cb694d9ed9cd0c3c *Meta/package.rds
0197ab1a2e7dbaf563907cf8a4a8aea6 *Meta/vignette.rds
8fd1feb263c021a915ede9f54c16a7a8 *NAMESPACE
a2ea4a2633d3887748149b11cce308f6 *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/MutationalPatterns
e517c544bdff7e98cd4d104ae5fb06ad *R/MutationalPatterns.rdb
89076effa2273df6428384b8c73308ce *R/MutationalPatterns.rdx
6e7ce860036bdec5a9ed5f391ea90650 *doc/Introduction_to_MutationalPatterns.R
2bb5e85303fbecc451f806e9d44a1f94 *doc/Introduction_to_MutationalPatterns.Rmd
66ae0b05af3572bad0feeb0a9eff51ac *doc/Introduction_to_MutationalPatterns.html
e9bb1b444c4e29bf8e7e40eafda3dc40 *doc/index.html
7c8f99f154f53b8a8318684ebc679756 *extdata/ReplicationDirectionRegions.bed
643092cb274fce36504f839500210821 *extdata/blood-AC.vcf
fc7938084ce8fbe9847d01bf118aa490 *extdata/blood-ACC55.vcf
150473517ba18e3aaf399c9b180c960b *extdata/blood-BCH.vcf
d9c3f2519867496f3ceb50fb74079ea8 *extdata/callableloci-sample.bed
e0c6f75c02472baeec73671bd90d4eb2 *extdata/colon1-sample.vcf
84ded44dfe7bc0bb9067596065d0ed83 *extdata/colon2-sample.vcf
6f9f28e32aa677c927a809b4b45617cd *extdata/colon3-sample.vcf
2c705176f6bd12f64c1fd67328140944 *extdata/empty.vcf
681b33009bfbd5e65e4844f9b77abb9f *extdata/intestine1-sample.vcf
ecd3e4f85e06319cae3c47a2b3c81bc9 *extdata/intestine2-sample.vcf
b2ee52aaed7098b2d404b401d14fe8ed *extdata/intestine3-sample.vcf
aed96a7a028a541e3c80d11aec1c17dd *extdata/liver1-sample.vcf
ae11d2abb6f40cc46e5270fe3517c807 *extdata/liver2-sample.vcf
2c1c91d75b873eccffe8903452940c5f *extdata/liver3-sample.vcf
e793c1c5a782b4772fdf69da34222ef3 *extdata/signatures/SIGNAL_conversion_matrix.txt
a184291fa592ded29fb6afddc2ef988f *extdata/signatures/dbs_COSMIC_reference.txt
5e052965ee25f874cd1c9082ed37e694 *extdata/signatures/dbs_SIGNAL_exposure.txt
71fcffe1378db7d61ae8e23d1d670cbb *extdata/signatures/indel_COSMIC_reference.txt
9e868e8eb41b0d2545ed168d034ba9c9 *extdata/signatures/snv_COSMIC_reference.txt
5ad31ce61e64b1ab1098f7d05130fc52 *extdata/signatures/snv_SIGNAL_exposure.txt
9ee9b09a6d6feb0fc153f30863ab9466 *extdata/signatures/snv_SIGNAL_reference.txt
fe868420f878f439498981e8e039ce10 *extdata/signatures/snv_SIGNAL_tissue.txt
fe9e67dbb125a7400885ec628cf9328a *extdata/signatures/snv_SPARSE_reference.txt
8048639b0d0fbc89dbee8b06dccbd560 *extdata/signatures/tsb_snv_COSMIC_reference.txt
fcb725007fc6fb02c72133cedfa170a5 *help/AnIndex
7a64c3d85e56059f2b212df7e6441536 *help/MutationalPatterns.rdb
e893388e96c628c05cba70fd28b71296 *help/MutationalPatterns.rdx
f83a5400f5911e379cb68422fc74604d *help/aliases.rds
e629b56ddf8d9c6a84a3d5610ee26ae1 *help/paths.rds
f2b66d2dc7f3eb5265a40dc132406fc2 *html/00Index.html
ff1a35c6482bbc90d8b496f86bf5ad31 *html/MutationalPatterns-defunct.html
9299a999a9ae24fad6e9f166e01b9c50 *html/MutationalPatterns-package.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
967d7504619aa69c520264ec1a1c5e13 *html/bin_mutation_density.html
2dae4d9d3df0dee5d9294eb54a7d40e7 *html/binomial_test.html
b66c0219e40737f0e614612a9e3b2008 *html/calculate_lesion_segregation.html
7998d7068a319b566268ae8d34dd01fe *html/cluster_signatures.html
5dc9f512c4eb733965749a571d794ab8 *html/context_potential_damage_analysis.html
14f9f5911a8ebca6d858842e956a27ff *html/convert_sigs_to_ref.html
8a59e1249633aefa8e8a878b1639bc25 *html/cos_sim.html
274497c52f43e375eb2b4c547fb4489f *html/cos_sim_matrix.html
5c2b0033a313bd8495afa59ebe40df25 *html/count_dbs_contexts.html
9c31f10254edff78ec5e28fde1046d25 *html/count_indel_contexts.html
3df381a799a8cb0584ffc5ceb6f58bb0 *html/count_mbs_contexts.html
ee454c8e1125dd0474967a09096fe478 *html/enrichment_depletion_test.html
1b9c7d88104c20c1b1d03a7d1a4cd0a6 *html/extract_signatures.html
6339bb73a6b067ead3a25b41971385d8 *html/fit_to_signatures.html
bfc31293341aa85d9963c4e22b5dac08 *html/fit_to_signatures_bootstrapped.html
3eee36463f5eb1a6d04f38e8344ac579 *html/fit_to_signatures_strict.html
92b35744d4068671d215492db92721a0 *html/genomic_distribution.html
e2019225b155a9a4c9d646f2620f6712 *html/get_dbs_context.html
3b1e0456281e9ffd0780a61e8f76a937 *html/get_indel_context.html
5b70488ba4973467f727b56d0b43180a *html/get_known_signatures.html
182d058022f8a9b978d5573b563fa9d9 *html/get_mut_type.html
fe5c9599ed1f722ba7328afe11e93fe7 *html/lengthen_mut_matrix.html
579d3d6ae16f28295bf54604e1ed8074 *html/merge_signatures.html
bf6f760a81c97b1fda59530fca931f3a *html/mut_192_occurrences.html
3bbb42143310e12fbe0f7c1f884394cd *html/mut_96_occurrences.html
162521aebcbac4f5eabba8881e9c47ff *html/mut_context.html
00cc6336198a90b55372019ac7c1f33a *html/mut_matrix.html
3fb78642eb4216fab2adfbed067ac1e8 *html/mut_matrix_stranded.html
62b2b31adcc1a37cde071d63370c7237 *html/mut_strand.html
407d37c704fb20879bf4e5ad26eaa720 *html/mut_type.html
5cd9084690fa1b563ef3eca7bd33c422 *html/mut_type_occurrences.html
5924dcf2e85dec1a1aad31bf1dbc223a *html/mutations_from_vcf.html
6e019b956838bf96b72da19f0e982779 *html/plot_192_profile.html
99eab948694eb52d03435974ad6e4e06 *html/plot_96_profile.html
1cb0c1ae724dd06a0174abb39500a2ff *html/plot_bootstrapped_contribution.html
3195e85cddec44ccd574b6b1e2ee4e54 *html/plot_compare_dbs.html
04517ee7062bf785b48bfe4dada0b31d *html/plot_compare_indels.html
06915016a78bc3cd1dae4535b3238fda *html/plot_compare_mbs.html
5a3b15e77b63b4c650398d6407f08ef4 *html/plot_compare_profiles.html
45928f9f64dced1ce1e200dc2cff5a96 *html/plot_contribution.html
64b1893bead12ddbd2184434856675b9 *html/plot_contribution_heatmap.html
fe85cddba9f6cf2648dec9eac184d500 *html/plot_correlation_bootstrap.html
2725eea19dc63469488e05a05e07368d *html/plot_cosine_heatmap.html
66c484013e3b524d07409112d12dc6f3 *html/plot_dbs_contexts.html
3867f28adb2ad3517320c85ac5bcac16 *html/plot_enrichment_depletion.html
c57322963ecc371cd312cbf9bd8575de *html/plot_indel_contexts.html
5542da8af5efdef0e91a18fc63acd4a2 *html/plot_lesion_segregation.html
edae16f64ca4bf164426bf92a9be407e *html/plot_main_dbs_contexts.html
bb43bbf51a47008dd2fd4a732273ba7f *html/plot_main_indel_contexts.html
e43439608459b1b7b1e822752691ae87 *html/plot_mbs_contexts.html
0267c4557271b5992cef7bcda5eda2e5 *html/plot_original_vs_reconstructed.html
ec7a1a78e1a9ca6ada52d25aa79a30ac *html/plot_profile_heatmap.html
0a8efb7895893d04776e3dd0c6e5cfe0 *html/plot_profile_region.html
e4a231f500b407f2b71fbd4cb5f2dbf7 *html/plot_rainfall.html
b45a3a7022461446e22a2bbdcdbc2038 *html/plot_river.html
ffc1c23fc198a7b6a17840567a6af4f6 *html/plot_signature_strand_bias.html
a4481ef79a9a85ceada92c176e82409e *html/plot_spectrum.html
72a1fc3348b4ae8120f2d34efc24009e *html/plot_spectrum_region.html
11b7c186cb9a0c7fa6e91b7d16fe5c73 *html/plot_strand.html
c3302cb7da0cd0e7805c77e1c81aa896 *html/plot_strand_bias.html
23074e6949ee6ab9e9c6ffe8111b382a *html/pool_mut_mat.html
95d13d5609c34174893d95a1a0aa25f9 *html/read_vcfs_as_granges.html
15a728deb7ee9c1cff441999698a83d8 *html/rename_nmf_signatures.html
13b2baef763e5c615d9c9e4318db0f24 *html/signature_potential_damage_analysis.html
c7b0f9e430a55a6cc0145425af671110 *html/split_muts_region.html
2b2b00d01a71837b196a75ca9051819a *html/strand_bias_test.html
7395b0d18ca8af44c19e12a18773491b *html/strand_occurrences.html
a3be19659b3711f2d2e223321fb838a5 *html/type_context.html
e9a4b533526e441eeea80933afd46290 *scripts/Format_signatures.R
d2d6c11b0390efcc8ce234fc87d4875e *scripts/create_example_dbs.R
6673fa4acea44331de0fec3bce32fec4 *scripts/create_example_indels.R
a45390662576f0de8ecc64eed8788ed0 *scripts/create_example_mbs.R
99ae1839a18e69d389a3733a6527e800 *scripts/create_example_regulatory_regions.R
556ed983fd8f1087510014aeb4bb6657 *scripts/create_example_snvs.R
ff19380799a4ddd931e386395ecedced *scripts/create_example_vcfs.R
634298b7a9cc0d3b65dc57ae3b8c0c14 *states/CTCF_g_data.rds
d6b322652e615904701ef72e4c44459c *states/blood_dbs_counts.rds
b0af1dc752f767eee9fa22d15df1da8a *states/blood_grl.rds
d7d87ca79521e46264814bc1c5f67405 *states/blood_grl_dbs.rds
b580d3c41f9eec304b8c0680385d05f2 *states/blood_grl_dbs_context.rds
4b264259f59199ed5b6993496a428fcd *states/blood_grl_indel.rds
f8d1e9284e9785cdc87da0699742ab5b *states/blood_grl_indel_context.rds
0bd14b1729b8f32696e25d1146bbfa5a *states/blood_grl_mbs.rds
3cee41ad4624f1c06124978d8cb69115 *states/blood_indel_counts.rds
a7314df33e94bde3c554a171fc8f565d *states/blood_indels_counts_split_region.rds
a3293e4bce27e93f4a7bfb6e6939e67e *states/blood_indels_longmatrix_split_region.rds
ac729851b5f2fdc6ce558da753568541 *states/blood_mbs_counts.rds
184ec97c6480f951678512f6cabd1aed *states/blosum62.rds
864049e3c0891475f859992e8f5b4050 *states/bootstrapped_snv_refit.rds
e0fa83f772e9e2518d5b81759de549be *states/context_mismatches.rds
98075b3a356f862af12d310e048596ea *states/dbs_refit.rds
7061ab2bf5880700c741b4a26e1a0361 *states/distr_data.rds
820a6629b78365b317fbdc845238cc8d *states/grl_split_region.rds
8c9fbf046102697209d7e5d6112de823 *states/indel_refit.rds
1f082d175526f3d0f0a6f919faea7f79 *states/lesion_segregation.rds
a7852b9d11241d49ab9abbe9040fd861 *states/mut_mat_data.rds
9d5ac4c45b8f597e8a8910cf8f7a08e1 *states/mut_mat_data_extended.rds
94bee7c42eb7688790dbeeb4506e3c7d *states/mut_mat_longregions.rds
a722830dde4d647868b52f92dc4f5208 *states/mut_mat_repli.rds
1724d53448820e24b0ed8a5702bba8f1 *states/mut_mat_s_data.rds
078f2c50a6ed1dfd7d8455549919173f *states/mut_mat_splitregions.rds
84527f56cc8efd5e749947aa2cb37bb4 *states/nmf_res_data.rds
ba6921b8d3702ccf19a234ed3d860ac3 *states/nmf_res_strand_data.rds
ed9e4d7ea30f09aaab6e675a954b0714 *states/promoter_flanking_g_data.rds
546ba8475a829565ac04648b6a9600a2 *states/promoter_g_data.rds
f0f6acfc617057ea0ea1a5026071a7b9 *states/read_vcfs_as_granges_output.rds
4722c5eeab118da611e41c53cd35e1f1 *states/regulatory_data.rds
5c2014ce303ad6959ba4a9a587102565 *states/repli_strand.rds
b441b89227245a00a0900bf6ff44c688 *states/snv_refit.rds
4ef3c51f0546149c803ba7c779efdf33 *states/strict_snv_refit.rds
