Files in campbio/musicatk
Mutational Signature Comprehensive Analysis Toolkit
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/annotate_variants.R
R/compare_results.R
R/cosmic_data.R
R/differential_analysis.R
R/discovery_prediction.R
R/kmeans.R
R/load_data.R
R/main_class.R
R/methods.R
R/misc_functions.R
R/musicatk.R
R/plot_exposures.R
R/plot_heatmap.R
R/plotting.R
R/standard_tables.R
R/table_utils.R
R/test_data.R
R/umap.R
R/utils-pipe.R
README.md
_pkgdown.yml
codecov.yml
data/cosmic_v2_sigs.rda
data/cosmic_v3_dbs_sigs.rda
data/cosmic_v3_indel_sigs.rda
data/cosmic_v3_sbs_sigs.rda
data/cosmic_v3_sbs_sigs_exome.rda
data/dbs_musica.rda
data/indel_musica.rda
data/musica.rda
data/musica_annot.rda
data/musica_sbs96.rda
data/musica_sbs96_tiny.rda
data/rep_range.rda
data/res.rda
data/res_annot.rda
docs/404.html
docs/articles/articles/installation.html
docs/articles/articles/installation_files/accessible-code-block-0.0.1/empty-anchor.js
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docs/articles/articles/installation_files/header-attrs-2.14/header-attrs.js
docs/articles/articles/installation_files/header-attrs-2.7/header-attrs.js
docs/articles/articles/tutorial_tcga_cnsl.html
docs/articles/articles/tutorial_tcga_cnsl_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/articles/tutorial_tcga_cnsl_files/crosstalk-1.1.1/css/crosstalk.css
docs/articles/articles/tutorial_tcga_cnsl_files/crosstalk-1.1.1/js/crosstalk.js
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docs/articles/articles/tutorial_tcga_cnsl_files/figure-html/exposure_heatmap_annot-1.png
docs/articles/articles/tutorial_tcga_cnsl_files/figure-html/exposure_heatmap_sigs-1.png
docs/articles/articles/tutorial_tcga_cnsl_files/figure-html/exposures_prop-1.png
docs/articles/articles/tutorial_tcga_cnsl_files/figure-html/exposures_raw-1.png
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docs/articles/articles/tutorial_tcga_cnsl_files/figure-html/name_sigs-1.png
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docs/articles/articles/ui_screenshots/AnnotationsTab.jpg
docs/articles/articles/ui_screenshots/CompareTab.jpg
docs/articles/articles/ui_screenshots/CompareTable.jpg
docs/articles/articles/ui_screenshots/DAOptions.jpg
docs/articles/articles/ui_screenshots/DATab.jpg
docs/articles/articles/ui_screenshots/DiscoverTab.jpg
docs/articles/articles/ui_screenshots/PredictDropdown.jpg
docs/articles/articles/ui_screenshots/PredictOptions.jpg
docs/articles/articles/ui_screenshots/PredictTab.jpg
docs/articles/articles/ui_screenshots/TCGA.jpg
docs/articles/articles/ui_screenshots/TableTab.jpg
docs/articles/articles/ui_screenshots/WilcoxonTable.jpg
docs/articles/articles/ui_screenshots/annotation_file.jpg
docs/articles/articles/ui_screenshots/cluster1.jpg
docs/articles/articles/ui_screenshots/cluster2.jpg
docs/articles/articles/ui_screenshots/cluster_tbl.jpg
docs/articles/articles/ui_screenshots/cluster_visual.jpg
docs/articles/articles/ui_screenshots/combine-table.jpg
docs/articles/articles/ui_screenshots/create_musica.jpg
docs/articles/articles/ui_screenshots/create_musica1.jpg
docs/articles/articles/ui_screenshots/download.jpg
docs/articles/articles/ui_screenshots/exp_box_setting1.jpg
docs/articles/articles/ui_screenshots/exp_box_setting2.jpg
docs/articles/articles/ui_screenshots/exp_box_setting3.jpg
docs/articles/articles/ui_screenshots/exp_plot1.jpg
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inst/extdata/public_LUAD_TCGA-97-7938.vcf
inst/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf
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inst/extdata/public_TCGA.LUSC.maf
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inst/script/example_data.R
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inst/shiny/server_tables.R
inst/shiny/style.CSS
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inst/shiny/ui_download.R
inst/shiny/ui_genome.R
inst/shiny/ui_heatmap.R
inst/shiny/ui_help.R
inst/shiny/ui_import.R
inst/shiny/ui_import_musica.R
inst/shiny/ui_import_tcga.R
inst/shiny/ui_musica.R
inst/shiny/ui_predict.R
inst/shiny/ui_resultvisualization.R
inst/shiny/ui_tables.R
man/add_flank_to_variants.Rd
man/add_variant_type.Rd
man/annotate_replication_strand.Rd
man/annotate_transcript_strand.Rd
man/annotate_variant_length.Rd
man/annotate_variant_type.Rd
man/auto_predict_grid.Rd
man/auto_subset_sigs.Rd
man/build_custom_table.Rd
man/build_standard_table.Rd
man/built_tables.Rd
man/cluster_exposure.Rd
man/combine_count_tables.Rd
man/combine_predict_grid.Rd
man/compare_cosmic_v2.Rd
man/compare_cosmic_v3.Rd
man/compare_results.Rd
man/cosmic_v2_sigs.Rd
man/cosmic_v2_subtype_map.Rd
man/cosmic_v3_dbs_sigs.Rd
man/cosmic_v3_indel_sigs.Rd
man/cosmic_v3_sbs_sigs.Rd
man/cosmic_v3_sbs_sigs_exome.Rd
man/count_table-class.Rd
man/create_dbs78_table.Rd
man/create_musica.Rd
man/create_sbs192_table.Rd
man/create_sbs96_table.Rd
man/create_umap.Rd
man/dbs_musica.Rd
man/discover_signatures.Rd
man/dot-jsd.Rd
man/drop_annotation.Rd
man/exposure_differential_analysis.Rd
man/exposures.Rd
man/extract_count_tables.Rd
man/extract_variants.Rd
man/extract_variants_from_maf.Rd
man/extract_variants_from_maf_file.Rd
man/extract_variants_from_matrix.Rd
man/extract_variants_from_vcf.Rd
man/extract_variants_from_vcf_file.Rd
man/generate_result_grid.Rd
man/get_musica.Rd
man/indel_musica.Rd
man/k_select.Rd
man/musica-class.Rd
man/musica.Rd
man/musica_annot.Rd
man/musica_result-class.Rd
man/musica_result_grid-class.Rd
man/musica_sbs96.Rd
man/musica_sbs96_tiny.Rd
man/musicatk.Rd
man/name_signatures.Rd
man/pipe.Rd
man/plot_cluster.Rd
man/plot_differential_analysis.Rd
man/plot_exposures.Rd
man/plot_heatmap.Rd
man/plot_sample_counts.Rd
man/plot_sample_reconstruction_error.Rd
man/plot_signatures.Rd
man/plot_umap.Rd
man/predict_exposure.Rd
man/rc.Rd
man/rep_range.Rd
man/res.Rd
man/res_annot.Rd
man/samp_annot.Rd
man/sample_names.Rd
man/select_genome.Rd
man/signatures.Rd
man/subset_musica_by_annotation.Rd
man/subset_musica_by_counts.Rd
man/subset_variant_by_type.Rd
man/subset_variants_by_samples.Rd
man/table_96.Rd
man/table_selected.Rd
man/tables.Rd
man/umap.Rd
man/variants.Rd
tests/testthat.R
tests/testthat/test-differentialanalysis.R
tests/testthat/test-heatmap.R
tests/testthat/test-kmeans.R
tests/testthat/test-load-vcf.R
tests/testthat/test-plotting.R
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vignettes/articles/MANIFEST.txt
vignettes/articles/installation.Rmd
vignettes/articles/tutorial_tcga_cnsl.Rmd
vignettes/articles/tutorial_tcga_ui.Rmd
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vignettes/musicatk.Rmd
