API for musicatk
Mutational Signature Comprehensive Analysis Toolkit
| Global functions | |
|---|---|
| %>% | Man page |
| .addSmallLegend | Source code |
| .add_annotation_to_df | Source code |
| .check_headers | Source code |
| .check_variant_genome | Source code |
| .check_variant_ref_in_genome | Source code |
| .cosine | Source code |
| .cosineDist | Source code |
| .count1 | Source code |
| .count2_del | Source code |
| .count2_ins | Source code |
| .count_repeat | Source code |
| .create_count_table | Source code |
| .discrete_colors | Source code |
| .extract_count_table | Source code |
| .get_indel_motifs | Source code |
| .gg_color_hue | Source code |
| .gg_default_theme | Source code |
| .jsd | Man page Source code |
| .kld | Source code |
| .micro_left | Source code |
| .micro_right | Source code |
| .multi_modal_discovery | Source code |
| .pivot_exposures | Source code |
| .pivot_signatures | Source code |
| .plot_compare_result_signatures | Source code |
| .required_maf_headers | Source code |
| .required_musica_headers | Source code |
| .table_exists_warning | Source code |
| add_flank_to_variants | Man page Source code |
| add_variant_type | Man page Source code |
| annotate_replication_strand | Man page Source code |
| annotate_transcript_strand | Man page Source code |
| annotate_variant_length | Man page Source code |
| annotate_variant_type | Man page Source code |
| auto_predict_grid | Man page Source code |
| auto_subset_sigs | Man page Source code |
| build_custom_table | Man page Source code |
| build_standard_table | Man page Source code |
| combine_count_tables | Man page Source code |
| combine_predict_grid | Man page Source code |
| compare_cosmic_v2 | Man page Source code |
| compare_cosmic_v3 | Man page Source code |
| compare_results | Man page Source code |
| cosmic_v2_sigs | Man page |
| cosmic_v2_subtype_map | Man page Source code |
| cosmic_v3_dbs_sigs | Man page |
| cosmic_v3_indel_sigs | Man page |
| cosmic_v3_sbs_sigs | Man page |
| cosmic_v3_sbs_sigs_exome | Man page |
| count_table-class | Man page |
| create_dbs_table | Man page Source code |
| create_indel_table | Source code |
| create_musica | Man page Source code |
| create_sbs192_table | Man page Source code |
| create_sbs96_table | Man page Source code |
| create_umap | Man page Source code |
| dbs_musica | Man page |
| discover_signatures | Man page Source code |
| drop_annotation | Man page Source code |
| drop_count_table | Source code |
| drop_na_variants | Source code |
| exposures | Man page |
| exposures,musica_result-method | Man page |
| exposures<- | Man page |
| exposures<-,musica_result,matrix-method | Man page |
| extract_count_tables | Man page Source code |
| extract_variants | Man page Source code |
| extract_variants_from_maf | Man page Source code |
| extract_variants_from_maf_file | Man page Source code |
| extract_variants_from_matrix | Man page Source code |
| extract_variants_from_vcf | Man page Source code |
| extract_variants_from_vcf_file | Man page Source code |
| generate_result_grid | Man page Source code |
| get_annot_tab | Source code |
| get_color_mapping | Source code |
| get_count_features | Source code |
| get_count_table | Source code |
| get_count_type | Source code |
| get_grid_list | Source code |
| get_grid_params | Source code |
| get_grid_table | Source code |
| get_result_type | Source code |
| get_tab_name | Source code |
| indel_musica | Man page |
| lda_posterior | Source code |
| musica | Man page |
| musica,musica_result-method | Man page |
| musica-class | Man page |
| musica_annot | Man page |
| musica_result-class | Man page |
| musica_result_grid-class | Man page |
| musica_sbs96 | Man page |
| musica_sbs96_tiny | Man page |
| name_signatures | Man page Source code |
| overwrite_samp_annot | Source code |
| plot_exposures | Man page Source code |
| plot_sample_counts | Man page Source code |
| plot_sample_reconstruction_error | Man page Source code |
| plot_signatures | Man page Source code |
| plot_umap | Man page Source code |
| predict_decompTumor2Sig | Source code |
| predict_exposure | Man page Source code |
| rc | Man page Source code |
| reconstruct_sample | Source code |
| rep_range | Man page |
| res | Man page |
| res_annot | Man page |
| samp_annot | Man page |
| samp_annot,musica-method | Man page |
| samp_annot,musica_result-method | Man page |
| samp_annot<- | Man page |
| samp_annot<-,musica,character,vector-method | Man page |
| samp_annot<-,musica_result,character,vector-method | Man page |
| sample_names | Man page |
| sample_names,musica-method | Man page |
| sample_names,musica_result-method | Man page |
| select_genome | Man page Source code |
| set_grid_list | Source code |
| set_grid_params | Source code |
| set_grid_table | Source code |
| sig_compare | Source code |
| signatures | Man page |
| signatures,musica_result-method | Man page |
| signatures<- | Man page |
| signatures<-,musica_result,matrix-method | Man page |
| subset_count_tables | Source code |
| subset_musica_by_annotation | Man page Source code |
| subset_musica_by_counts | Man page Source code |
| subset_variant_by_type | Man page Source code |
| subset_variants_by_samples | Man page Source code |
| table_96 | Man page Source code |
| table_name | Man page |
| table_name,musica_result-method | Man page |
| tables | Man page |
| tables,musica-method | Man page |
| tables,musica_result-method | Man page |
| tables<- | Man page |
| tables<-,musica,list-method | Man page |
| umap | Man page |
| umap,musica_result-method | Man page |
| umap<- | Man page |
| umap<-,musica_result,matrix-method | Man page |
| variants | Man page |
| variants,musica-method | Man page |
| variants,musica_result-method | Man page |
| variants<- | Man page |
| variants<-,musica,data.table-method | Man page |
| whichSignatures | Source code |
