Files in musicatk

Mutational Signature Comprehensive Analysis Toolkit

NEWS.md README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

data/rep_range.rda

data/musica_sbs96_tiny.rda

data/musica_sbs96.rda

data/cosmic_v3_sbs_sigs_exome.rda

data/res.rda

data/dbs_musica.rda

data/cosmic_v3_indel_sigs.rda

data/cosmic_v3_sbs_sigs.rda

data/indel_musica.rda

data/cosmic_v3_dbs_sigs.rda

data/res_annot.rda

data/musica.rda

data/cosmic_v2_sigs.rda

data/musica_annot.rda

R/discovery_prediction.R R/load_data.R

R/sysdata.rda

R/misc_functions.R R/cosmic_data.R R/table_utils.R R/test_data.R R/utils-pipe.R R/annotate_variants.R R/umap.R R/compare_results.R R/plotting.R R/main_class.R R/methods.R R/plot_exposures.R R/standard_tables.R vignettes/musicatk.Rmd man/subset_musica_by_counts.Rd man/subset_variants_by_samples.Rd man/table_name.Rd man/combine_count_tables.Rd man/musica_result_grid-class.Rd man/extract_variants_from_vcf_file.Rd man/compare_cosmic_v3.Rd man/plot_sample_counts.Rd man/rc.Rd man/auto_subset_sigs.Rd man/name_signatures.Rd man/annotate_variant_type.Rd man/signatures.Rd man/extract_variants_from_matrix.Rd man/create_musica.Rd man/create_sbs96_table.Rd man/extract_variants_from_maf_file.Rd man/musica.Rd man/pipe.Rd man/samp_annot.Rd man/build_custom_table.Rd man/cosmic_v3_indel_sigs.Rd man/subset_musica_by_annotation.Rd man/res.Rd man/cosmic_v3_sbs_sigs_exome.Rd man/tables.Rd man/extract_variants.Rd man/res_annot.Rd man/exposures.Rd man/cosmic_v3_dbs_sigs.Rd man/musica-class.Rd man/plot_umap.Rd man/extract_variants_from_vcf.Rd man/annotate_transcript_strand.Rd man/annotate_variant_length.Rd man/count_table-class.Rd man/predict_exposure.Rd man/plot_exposures.Rd man/annotate_replication_strand.Rd man/extract_count_tables.Rd man/plot_signatures.Rd man/auto_predict_grid.Rd man/add_variant_type.Rd man/indel_musica.Rd man/drop_annotation.Rd man/cosmic_v2_sigs.Rd man/dbs_musica.Rd man/sample_names.Rd man/table_96.Rd man/cosmic_v3_sbs_sigs.Rd man/create_dbs_table.Rd man/cosmic_v2_subtype_map.Rd man/compare_results.Rd man/add_flank_to_variants.Rd man/umap.Rd man/musica_sbs96_tiny.Rd man/rep_range.Rd man/compare_cosmic_v2.Rd man/subset_variant_by_type.Rd man/select_genome.Rd man/variants.Rd man/extract_variants_from_maf.Rd man/discover_signatures.Rd man/build_standard_table.Rd man/musica_result-class.Rd man/create_umap.Rd man/musica_sbs96.Rd man/create_sbs192_table.Rd man/plot_sample_reconstruction_error.Rd man/dot-jsd.Rd man/generate_result_grid.Rd man/combine_predict_grid.Rd man/musica_annot.Rd tests/testthat.R tests/testthat/test-plotting.R tests/testthat/test-signatures.R tests/testthat/test-load-vcf.R inst/doc/musicatk.Rmd inst/doc/musicatk.R

inst/doc/musicatk.html

inst/extdata/public_SKCM_TCGA-ER-A19O-06A-11D-A197-08.vcf

inst/extdata/public_SKCM_TCGA-ER-A197-06A-32D-A197-08.vcf

inst/extdata/sample_annotations.txt

inst/extdata/public_SKCM_TCGA-EE-A3J5-06A-11D-A20D-08.vcf

inst/extdata/public_TCGA.LUSC.maf

inst/extdata/public_LUAD_TCGA-97-7938.vcf

inst/script/example_data.R

musicatk documentation built on Nov. 8, 2020, 5:16 p.m.