c824d1811d4ef46305ff64283c72d6b3 *DESCRIPTION
eedd6ccd52439465e1cb52688ccc6371 *NAMESPACE
5baabcc2339584b8d94758ac418b79e5 *NEWS.md
f35eb6c64cce854a8c1a6eb979359097 *R/annotate_variants.R
942cf1a5867969b54848b1274e5a434e *R/class_count_table.R
a064f1cb8fd5bf187e280229376b28b7 *R/class_musica.R
c2b35243fdcf5d953e7768769a0f8058 *R/class_result_collection.R
ac056a19a83ca735966d47fd1dec028b *R/class_result_model.R
c900fb42d06708d2e72a98474c6cb437 *R/compare_results.R
75571e6cb57aa1af5db104c0303843f7 *R/cosmic_data.R
7111e6efe1018d234be8e8bd144dbadd *R/differential_analysis.R
dbc592bc8de764d815e30f40366ad658 *R/discovery_prediction.R
b990f1c0b9632d9d2ffacdb61355d2d1 *R/k_val_assit.R
91fc482a83a789984f73329d987a87c3 *R/kmeans.R
04f32b43760f089cb90cae370615b95f *R/load_data.R
2360c50cda02c8fd2d10d02a39e3ffd5 *R/misc_functions.R
c03406335c3a3d56ca7bfdd305167239 *R/musicatk.R
7013df93656f6b410f79c7b7d472cc6d *R/plot_exposures.R
9fc047cc326c9d84f2879fc42a7bfd1c *R/plot_heatmap.R
5df8fc038f6b0046e234189179e77cae *R/plot_sample_counts.R
ca4b871a1287ba513921b0084f9a773a *R/plot_sample_reconstruction_error.R
779dd7c15304b11ad85c5c7b1149b15a *R/plot_signatures.R
9479856da4b09c643b8c614dd0a5ff7a *R/plotting.R
36835636f6366105332b2e3599d2cb36 *R/standard_tables.R
63ab968dcf81c599dfee0afbae76a9a4 *R/table_utils.R
c825ef8672875f5e189f484c9108ed9d *R/test_data.R
56d19838882ee2a322f1906b98048dd6 *R/umap.R
2c5e45654ec0e77cdb198a6de4d8a04f *R/utils-pipe.R
ce89d0f15e8282a0020cd563bd5f34e3 *README.md
0a00be6f51e0060419240c80663a1cf2 *build/vignette.rds
8f28d28132124649c40d91d262c64ec2 *data/cosmic_v2_sigs.rda
9b0254ebb6bcd9909c7def85d252ca88 *data/cosmic_v3_dbs_sigs.rda
0cd0458a9d301b5c5f1d1d4eff91fc66 *data/cosmic_v3_indel_sigs.rda
444dd5c647a8d9dbb9e46bbce9c5fd0e *data/cosmic_v3_sbs_sigs.rda
c80badb78a89d31cddac30b578bb6362 *data/cosmic_v3_sbs_sigs_exome.rda
73aa02064495f98719d3d0a7209b0198 *data/dbs_musica.rda
dd571480cd62b1b1cf1c8ef5cedb8783 *data/indel_musica.rda
a2a04bd3c00ccab2410e4400c3b6833c *data/musica.rda
4f14bb829a65a58ca28a97367b82d202 *data/musica_annot.rda
e7133f3f13b41be438a3b00e5bcc87fe *data/musica_sbs96.rda
e567f195f0224cee7e4794eaef1c6cc7 *data/musica_sbs96_tiny.rda
34dbaa85293fe71e431d30ba6ad030a6 *data/rep_range.rda
9898173eca8084e589c9b1d69d339202 *data/res.rda
a6dee5f67ca2a85104ee0ede17c2a0bf *data/res_annot.rda
aebf469e9415805a66943576230c4a34 *inst/doc/musicatk.R
b08784fc30f163a5243f6fc37a486333 *inst/doc/musicatk.Rmd
b88761a1752b6c47ca9246b67e377a17 *inst/doc/musicatk.html
4cbf7b3f857096a6090c9eb6cefd9dd2 *inst/extdata/luad_tcga_count_table.csv
e651b9f791d0c38f2bd45aca9864cef9 *inst/extdata/public_LUAD_TCGA-97-7938.vcf
15c6b74e55900b3c276db4cc3885f77f *inst/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf
3ea253273b24dd59a3016baee77ef91a *inst/extdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf
a6d9fec3bbf4ff3b47a76eb83ad724ed *inst/extdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf
37706ffefe7ff446358829c5d04a4ae4 *inst/extdata/public_TCGA.LUSC.maf
271456a707445309282c1460f964dd31 *inst/extdata/sample_annotations.txt
c075b3d5296b47786b6900eb09ff2053 *inst/script/example_data.R
3f776196299a727274c471cb96d04b53 *inst/shiny/MANIFEST.txt
75797c30b4999d7995e8e9ad90a41678 *inst/shiny/app.R
0ebcc52b04b69e241b4e8d3f0476eee8 *inst/shiny/server.R
b3ab21ba52644d26ee99394d2f681ccf *inst/shiny/server_tables.R
d41d8cd98f00b204e9800998ecf8427e *inst/shiny/style.CSS
b3c3902a7fdb9a262e8b6201976b4c39 *inst/shiny/ui.R
e64525e3b18b9be7a35e0a7e9f2a28d9 *inst/shiny/ui_annotations.R
8353e58721e60d151c1a9bb89a830ca2 *inst/shiny/ui_cluster.R
f1c6452e94d3556f9211e2c3256a2be7 *inst/shiny/ui_compare.R
e35827aa4688a1426c831e9f3d969503 *inst/shiny/ui_differentialanalysis.R
2e39f53648d6db0f0adf7aa77a109e68 *inst/shiny/ui_discover.R
9259b85905931e9ca69bbdaa97efdb3f *inst/shiny/ui_download.R
68b329da9893e34099c7d8ad5cb9c940 *inst/shiny/ui_genome.R
9fca71760585731f8cd95e790a067e01 *inst/shiny/ui_heatmap.R
29811851999dfa6ed28396d4b4168e0c *inst/shiny/ui_help.R
6f20176f17fdde74244c3d1d1a34cc37 *inst/shiny/ui_import.R
f35867b413ea79627ed6b4101ebc71be *inst/shiny/ui_import_musica.R
7ca49d98d326cfe555f73a2a3ddac0aa *inst/shiny/ui_import_tcga.R
624237bb8654da3f230350237553f22f *inst/shiny/ui_musica.R
1b5ffe0e41c8e8752147408618191d4f *inst/shiny/ui_predict.R
5f1d5a84805efc5b40f663e3b21ee142 *inst/shiny/ui_resultvisualization.R
dddda1c353e9860a318263961365838d *inst/shiny/ui_tables.R
b135cc146209b8fd6ae1e44ab3528984 *man/add_flank_to_variants.Rd
a73e60189cc12110e2b091f71d086e3f *man/add_result.Rd
0c63d30356d5508fd0a123ec8939eb8a *man/add_variant_type.Rd
c346c1cb31ebdb3036afc1263afcd65b *man/annotate_replication_strand.Rd
f9fc3d296f76b5d441569506b211e549 *man/annotate_transcript_strand.Rd
2df1e13fc2221144c49bbf587c596e40 *man/annotate_variant_length.Rd
1aa69adaecee07c8fde1419b324c5dee *man/annotate_variant_type.Rd
9149a32158a1eb9641e109dee2b06e90 *man/auto_predict_grid.Rd
46bf60dbd7da02d7cff6c61898489a98 *man/auto_subset_sigs.Rd
e2d0e8d90021b2a61c24714104ee91ea *man/build_custom_table.Rd
d830b65ff95278dda0a1d88c789bf641 *man/build_standard_table.Rd
da49804b89cc4c577db33af4dc60f02d *man/built_tables.Rd
efc413640c8215779c56bf12a1a69f15 *man/cluster_exposure.Rd
02a69e5ecc915829fc27463b294be486 *man/combine_count_tables.Rd
b459464b04e3611dbd2a7bd6d6351cad *man/combine_predict_grid.Rd
72ad8c650dca6d59f9b04ee778fef1fb *man/compare_cosmic_v2.Rd
c4d93d72db2e7b6f72dce089e0b0a96e *man/compare_cosmic_v3.Rd
a9ab48d35288e0b47231d0cbdb9ac68f *man/compare_k_vals.Rd
a3d42a05c85840c6ae8875d668b09ac6 *man/compare_results.Rd
7c4f23ac3c1b86ca36aec48f1b11f5ef *man/cosmic_v2_sigs.Rd
6e3c71eabdbfff1ee19b64b338215989 *man/cosmic_v2_subtype_map.Rd
d04b44f7880397db68a5b0853d597d4b *man/cosmic_v3_dbs_sigs.Rd
941a38fd1007df861603dacef82474f9 *man/cosmic_v3_indel_sigs.Rd
49bf822222df3bde5b8bed77032ceb49 *man/cosmic_v3_sbs_sigs.Rd
204b5e4c21dcdb25bd3571054a1743eb *man/cosmic_v3_sbs_sigs_exome.Rd
f023beae421a95876bea91e68f014d29 *man/count_table-class.Rd
0f3fe784f16f8f60f6acd3f10d4326a4 *man/create_dbs78_table.Rd
9c1e86aa8479d0ba76e8013831becb4c *man/create_musica_from_counts.Rd
41d5c4bcbf5c90817bf064535ea5f044 *man/create_musica_from_variants.Rd
4b2df6eb6302c9b4b62cab7e5a73f4c9 *man/create_sbs192_table.Rd
3425d7906a735b704a48c29c410d29f0 *man/create_sbs96_table.Rd
17fe9ab116edcaea910847991f1442d5 *man/create_umap.Rd
5d5c2b8e666be9e71e77f22e20f13b00 *man/credible_intervals.Rd
9f296f1cce84ad5f1c726dde0f84c798 *man/dbs_musica.Rd
504352ee80a6bf834717bd9618540311 *man/discover_signatures.Rd
aa04ed42a558ba956cdad76720b22eb4 *man/dot-jsd.Rd
0f09cfb282ee9a0a3fdfe1d760d4fd89 *man/drop_annotation.Rd
05eeae76f10f3713fd03bdccb7b6fd2b *man/exposure_differential_analysis.Rd
9e5b57e8ad25d67eb555af75ed57642b *man/exposures.Rd
e4afaa6c960f1d229bed4b7f5d82a056 *man/extract_count_tables.Rd
248db6dc7f67a810785564085ad373db *man/extract_variants.Rd
69032a731c20a00b20c7b08ad970a499 *man/extract_variants_from_maf.Rd
5b1a314a955b1ebfffa35120e869c018 *man/extract_variants_from_maf_file.Rd
a3a3a228edf992306ef455b0f0a382d3 *man/extract_variants_from_matrix.Rd
b37ce4f70370aa7e66e501123776e440 *man/extract_variants_from_vcf.Rd
4040840211bdd767ca69f8429614e0ab *man/extract_variants_from_vcf_file.Rd
661cff7569cf963d48d74ef643cec9f2 *man/generate_result_grid.Rd
43187c95db3b0b0c0c5c8ae3bba5dc3e *man/get_count_table.Rd
b672c5bb8a9180a0d8a12e9a26420047 *man/get_modality.Rd
0a4f2cef752f6eb19cf782756e719c03 *man/get_model.Rd
a05d15825c86a5896cbada61851b61ae *man/get_result_list_entry.Rd
89ee1c8ad5ee721c8dfe8f8104916153 *man/hyperparameter.Rd
deb01d416e110227dd92b62d3f399877 *man/indel_musica.Rd
17d2f2d86ae8ce563b0f28c5fa9f8e1e *man/k_select.Rd
ad4413ce869bf42801900a1a5ffd2168 *man/metrics.Rd
9817c9c59b0a7677ada05b06ef10fc7b *man/modality.Rd
bb5f5dce0799392e2e1118430f44bd4f *man/model_id.Rd
652676697c9912cf645aa9ff57a20ae1 *man/musica-class.Rd
0b8a806afe9f3fcd6a88dffd94a92fb0 *man/musica.Rd
c7f235b27fd42d452c965aa2504cce68 *man/musica_annot.Rd
7f9d45470ce8bf1d604882c05e1f1a68 *man/musica_sbs96.Rd
f6db1434a863fa8fe72c54931ca3bb8b *man/musica_sbs96_tiny.Rd
b140a2faab80a388431f2e52b60f5cee *man/musicatk.Rd
0e8c805fec08766513bdaf1e4ebc47ca *man/name_signatures.Rd
1c6629a3e20dfb9f710ee56a43f02275 *man/num_signatures.Rd
e184fc59ce22461c500edf19b2f94a6a *man/other_parameters.Rd
6b7847ec762393c04a59bc1923a4a5cf *man/parameter.Rd
ef248b6574d6131b007c52f4ebfb2ae2 *man/pipe.Rd
2caa35cf05abd25dbabfe9878ea85e42 *man/plot_cluster.Rd
20902819971bf285e03f0ef3e1ed2ef0 *man/plot_differential_analysis.Rd
938ba5402e451b9630b6665599011e1e *man/plot_exposures.Rd
adab97d49082ee6852160af977b1f66f *man/plot_heatmap.Rd
ce350e6b7631b847421ecd2a5fb818d8 *man/plot_k_comparison.Rd
14aa21f8f329ce9109ba500711c19739 *man/plot_sample_counts.Rd
a033a8a7fc6e2f62de2e4010b136b82b *man/plot_sample_reconstruction_error.Rd
d46df4f1ee2fa5038c0672815f6b3145 *man/plot_signatures.Rd
671ff6b4616cb3c7552731c7a94a59e8 *man/plot_umap.Rd
2f2a4d9f8ddae3265c6dad09e6abf6ac *man/predict_exposure.Rd
9a655110d6da939dea024f8294c27c84 *man/rc.Rd
f6ce8904a040d8c98babec150d635919 *man/rep_range.Rd
416727b7b82988638dd1000d1cb59754 *man/res.Rd
b7fd92bb4820b0590bc16d443d2c8659 *man/res_annot.Rd
779a0694cda71694b5808794ee399980 *man/result_collection-class.Rd
79a71db445888ac7dec4e60a04f9e8c7 *man/result_list.Rd
898ceeb9fb944f05a25071ab36088e7d *man/result_model-class.Rd
ba567b9cb46a809f72ed0053033d1ae5 *man/samp_annot.Rd
7fdaa8c09ef9255c30f2bfa08144236a *man/sample_names.Rd
34fa0dbc9eaff4b0ee1963a03980ffac *man/select_genome.Rd
bc73cb9ffdae8a6c50d732863751771e *man/signatures.Rd
2315bbb33495e6d732f97ac5ce91e14b *man/subset_musica_by_annotation.Rd
146e99cabd2803f8e277fda87effab70 *man/subset_musica_by_counts.Rd
5c9c55656ce65132b63d90f54f34651a *man/subset_variant_by_type.Rd
e9ab0711c0cced484fc1aa7c42475205 *man/subset_variants_by_samples.Rd
2226e286ddee169219d302589513e592 *man/table_96.Rd
2d040fa5ff4bb737b5c38eca7dac4a75 *man/table_selected.Rd
ef003530e7ea8f8089f9ae0097bafb69 *man/tables.Rd
3063b9ad9087a698281eb423e09a80da *man/umap.Rd
9db67573eb055377f18736efb8059715 *man/variants.Rd
5ecb87d96e783045015db57be67814f5 *tests/testthat.R
b9f5422028a2b9b0144e3ebf88ab5903 *tests/testthat/test-differentialanalysis.R
617c4e9858b6d15501080c511eb54585 *tests/testthat/test-heatmap.R
efc55aa58b9b9b855082d46648ca4ff0 *tests/testthat/test-kmeans.R
113c9804516fadb524323683f7a790c9 *tests/testthat/test-load-vcf.R
493bb0b118b6662d95dc853b072d6b5b *tests/testthat/test-plotting.R
ffb1f00a83c352bc23d0824b586a4b1d *tests/testthat/test-signatures.R
b35078be4f68101a1b0157ae8e6bd937 *vignettes/articles/MANIFEST.txt
684bd10ae8139970e18e659746dcb485 *vignettes/articles/installation.Rmd
2b9da1062890239004f1627fe6084310 *vignettes/articles/tutorial_tcga_cnsl.Rmd
7317b05a2a971032433afaf159bb21cd *vignettes/articles/tutorial_tcga_ui.Rmd
2a688d4624c42971e0b03654b761dd70 *vignettes/figures/compare_cosmic-1.png
fbb4c680977070a2cf852311fc21ecbb *vignettes/figures/exposures_prop-1.png
9f6dcbff611def5e7898ac44225c9412 *vignettes/figures/exposures_raw-1.png
fdde9f9608993dac9382b39ab5ecb983 *vignettes/figures/name_sigs-1.png
394a63cb7fbef60a309c5af73ac101df *vignettes/figures/plot_exposures_box_annot-1.png
472e88dd6188e7abac528fe3989ba00f *vignettes/figures/plot_exposures_box_sig-1.png
d1d954c1846857fd3de783835ec03af0 *vignettes/figures/plot_exposures_by_subtype-1.png
abc95feb468b162d4efe97123f1bae1e *vignettes/figures/plot_sigs-1.png
42dc868a51493c98d8db69a2addc3b5e *vignettes/figures/plotly-1.png
7c393bbfed51e109d18919afebc2e097 *vignettes/figures/plotly-2.png
de63e3ddb93f5bf5a9e730951eb3e697 *vignettes/figures/plotly-3.png
ba256b25631b4803b753338faf6c56e3 *vignettes/figures/predict_compare-1.png
27148484aebc98b496901af4c711fca8 *vignettes/figures/predict_cosmic-1.png
65e1e34fcc4f1fccffe7310ad702854c *vignettes/figures/sample_counts-1.png
a49a954806442a2379ed7c2c95400400 *vignettes/figures/umap_plot-1.png
0ef175cb3aa70c506fbf94e11bfb6ac0 *vignettes/figures/umap_plot_annot-1.png
d500abd22d6c6f921867582c910eeed9 *vignettes/figures/umap_plot_same_scale-1.png
b08784fc30f163a5243f6fc37a486333 *vignettes/musicatk.Rmd
a77160be06ab8e02675c122ba056e35a *vignettes/ui_screenshots/AnnotationOptions.jpg
d2ac78e44e448533f690934371ad2f0a *vignettes/ui_screenshots/AnnotationTable.jpg
bb3ce76e40ffd9c0b5b9efc58765cff6 *vignettes/ui_screenshots/AnnotationsTab.jpg
4bda6076c51d450b4abf73b685557ade *vignettes/ui_screenshots/CompareTab.jpg
62c767e3d10e238bbd1bebac7013faa3 *vignettes/ui_screenshots/CompareTable.jpg
c48283d4ee5c7950adb35bb7989024ec *vignettes/ui_screenshots/DAOptions.jpg
9e308d7a16db43bc541c2b6bc99d6caa *vignettes/ui_screenshots/DATab.jpg
73ba7cc991b0b7ddb60e0825f551176d *vignettes/ui_screenshots/DiscoverTab.jpg
1469ec8dd827a32a749f7feb03a4babc *vignettes/ui_screenshots/PredictDropdown.jpg
95978870edd5eb0ae1a326eea4f0a916 *vignettes/ui_screenshots/PredictOptions.jpg
3e06283f25484f648e8f8fdff36a388d *vignettes/ui_screenshots/PredictTab.jpg
ac147c0d92c6d09aa4a0db9167905e6e *vignettes/ui_screenshots/TCGA.jpg
9aa15bb462b9eb5a030336bcffe81480 *vignettes/ui_screenshots/TableTab.jpg
32bcea61367a8f184482106476bf2ac9 *vignettes/ui_screenshots/WilcoxonTable.jpg
ad3756e473128ee6301c5aa044edfe58 *vignettes/ui_screenshots/annotation_file.jpg
c9f1e0cfb458ba0e183fd227e91c6613 *vignettes/ui_screenshots/cluster1.jpg
ffc1e29a2a5aa0ca3aa95a8ab7ada816 *vignettes/ui_screenshots/cluster2.jpg
30442a295cbadb12991ee37e1fb30c1e *vignettes/ui_screenshots/cluster_tbl.jpg
3c9b9fef626de84791c0924457ff1ec7 *vignettes/ui_screenshots/cluster_visual.jpg
e729a18296f8c95dbcbe59a109875ca7 *vignettes/ui_screenshots/combine-table.jpg
1b3fe58f710ecdfc09668c635ab9ce1f *vignettes/ui_screenshots/create_musica.jpg
61dc5c6da1223b3b13de535cf08fdc39 *vignettes/ui_screenshots/create_musica1.jpg
ccf09974617950f8b0f26ea3f1abc8af *vignettes/ui_screenshots/download.jpg
996d8909a6998f0ae980b35e4e9c996b *vignettes/ui_screenshots/exp_box_setting1.jpg
b07759467ebfcf15d38ab1dcc21dd5a8 *vignettes/ui_screenshots/exp_box_setting2.jpg
bb4cd07876f333bbf3a4c720deeed459 *vignettes/ui_screenshots/exp_box_setting3.jpg
747c6a8d653521dc2a551a1a1ef9caae *vignettes/ui_screenshots/exp_plot1.jpg
07005633de18987e0ef38d45036b4133 *vignettes/ui_screenshots/exp_plot2.jpg
2b1ef1013ba6d6acc97dbb2b5675cd89 *vignettes/ui_screenshots/exp_plot3.jpg
8eadc4a459c68772ac171a4f8ac620fb *vignettes/ui_screenshots/exp_plot4.jpg
1672c2d9eb0097e9eebe3548a30b7db3 *vignettes/ui_screenshots/exp_plot5.jpg
a85328fa0572f882a0e0e3d5aba4b7d8 *vignettes/ui_screenshots/heatmap.jpg
9a1d2e445e96b4960235f7d485982a83 *vignettes/ui_screenshots/heatmap1.jpg
5f749dadf2e6f022830e89442c18bd02 *vignettes/ui_screenshots/import.jpg
f497a2f088537f8a09a7b4a5123e9ee4 *vignettes/ui_screenshots/import1.jpg
772de4aff0ff9be34a3e84a42b59505b *vignettes/ui_screenshots/import2.jpg
eb9480045662f0884aeb0ff8c38bd04b *vignettes/ui_screenshots/musicatk-Flowchart.jpg
4ee49f4486ee9796f5935ae2ae5c8e06 *vignettes/ui_screenshots/sig_plot.jpg
84f97749e74b5f0625922f74dd5fe8e4 *vignettes/ui_screenshots/sorting.jpg
28c52141eff3ba6e151b3c827a7d1d2c *vignettes/ui_screenshots/umap1.jpg
1e5a5dfc6e6ef3996b4061d311170ba9 *vignettes/ui_screenshots/umap2.jpg
598667a32d9273679087a5f33d1511d8 *vignettes/ui_screenshots/umap3.jpg
ef02a0d70c71119e6449158d16cabb68 *vignettes/ui_screenshots/upload_musica.jpg
b6518a152c32f5960c73cac852bc269b *vignettes/ui_screenshots/visual_exp.jpg
eb933d463309c4026c8c612a3973631a *vignettes/ui_screenshots/visual_sig.jpg
22e0cef3cd1dd05ca9f1382e5e987962 *vignettes/ui_screenshots/wss.jpg
