| add_flank_to_variants | Uses a genome object to find context and add it to the... |
| add_variant_type | Generates a variant type table |
| annotate_replication_strand | Add replication strand annotation to SBS variants based on... |
| annotate_transcript_strand | Add transcript strand annotation to SBS variants (defined in... |
| annotate_variant_length | Adds an annotation to the input musica's variant table with... |
| annotate_variant_type | Annotate variants with variant type ("SBS", "INS", "DEl",... |
| auto_predict_grid | Automatic filtering of signatures for exposure prediction... |
| auto_subset_sigs | Automatic filtering of inactive signatures |
| build_custom_table | Builds a custom table from specified user variants |
| build_standard_table | Builds count tables using various mutation type schemas |
| built_tables | Retrieve the names of count_tables from a musica object |
| cluster_exposure | Perform clustering analysis from a musica result object |
| combine_count_tables | Combines tables into a single table that can be used for... |
| combine_predict_grid | Combine signatures and exposures of different models.... |
| compare_cosmic_v2 | Compare a result object to COSMIC V2 SBS Signatures... |
| compare_cosmic_v3 | Compare a result object to COSMIC V3 Signatures; Select exome... |
| compare_k_vals | Compare k values |
| compare_results | Compare two result files to find similar signatures |
| cosmic_v2_sigs | COSMIC v2 SBS96 Signatures Result Object |
| cosmic_v2_subtype_map | Input a cancer subtype to return a list of related COSMIC... |
| cosmic_v3_dbs_sigs | COSMIC v3 DBS Genome Signatures Result Object |
| cosmic_v3_indel_sigs | COSMIC v3 Indel Genome Signatures Result Object |
| cosmic_v3_sbs_sigs | COSMIC v3 SBS96 Genome Signatures Result Object |
| cosmic_v3_sbs_sigs_exome | COSMIC v3 SBS96 Exome Signatures Result Object |
| count_table-class | Object containing the count table matrices, their names and... |
| create_dbs78_table | Creates and adds a table for standard doublet base... |
| create_musica_from_counts | Creates a musica object from a mutation count table |
| create_musica_from_variants | Creates a musica object from a variant table |
| create_result_model | Load an external model into a result_model object |
| create_sbs192_table | Uses a genome object to find context and generate standard... |
| create_sbs96_table | Uses a genome object to find context and generate standard... |
| create_umap | Create a UMAP from a model result |
| credible_intervals | Retrieve credible_intervals from a result_model,... |
| dbs_musica | dbs_musica |
| discover_signatures | Discover mutational signatures |
| dot-jsd | Calculates 1 - Jensen-Shannon Divergences between all pairs... |
| drop_annotation | Drops a column from the variant table that the user no longer... |
| exposure_differential_analysis | Compare exposures of annotated samples |
| exposures | Retrieve exposures from a result_model, result_collection, or... |
| extract_count_tables | Extract count tables list from a musica object |
| extract_variants | Extract variants from mutliple objects |
| extract_variants_from_maf | Extract variants from a maf object |
| extract_variants_from_maf_file | Extracts variants from a maf file |
| extract_variants_from_matrix | Extract variants from matrix or data.frame like objects |
| extract_variants_from_vcf | Extracts variants from a VariantAnnotation VCF object |
| extract_variants_from_vcf_file | Extracts variants from a vcf file |
| generate_result_grid | Generate result_grid from musica based on annotation and... |
| get_count_table | Retrieve count_table matrix from count_table object |
| get_modality | Retrieve a specific modality entry from a musica or... |
| get_model | Retrieve model from a musica or result collection object |
| get_result_list_entry | Retrieve result_list entry from a musica object |
| hyperparameter | Retrieve hyperparameter from a musica or result_collection... |
| indel_musica | indel_musica |
| k_select | Plots for helping decide number of clusters |
| metrics | Retrieve metrics from a result_model, result_collection, or... |
| modality | Retrieve modality from a result_model, result_collection, or... |
| model_id | Retrieve model_id from a result_model, result_collection, or... |
| musica | musica |
| musica_annot | musica_annot |
| musica-class | The primary object that contains variants, count_tables, and... |
| musica_sbs96 | musica_sbs96 |
| musica_sbs96_tiny | musica_sbs96_tiny |
| musicatk | Starts the musicatk interactive Shiny app |
| name_signatures | Rename signatures for a model |
| num_signatures | Retrieve num_signatures from a result_model,... |
| other_parameters | Retrieve other_parameters from a result_model,... |
| parameter | Retrieve parameter from a musica or result_collection object |
| pipe | Pipe operator |
| plot_cluster | Visualize clustering results |
| plot_differential_analysis | Compare exposures of annotated samples |
| plot_exposures | Display sample exposures with bar, box, or violin plots |
| plot_heatmap | Plot heatmaps using the exposures matrix |
| plot_k_comparison | Plot k comparison |
| plot_sample_counts | Plot distribution of sample counts |
| plot_sample_reconstruction_error | Plot reconstruction error for a sample |
| plot_signatures | Plots the mutational signatures |
| plot_umap | Plot a UMAP from a musica result |
| predict_exposure | Prediction of exposures in new samples using pre-existing... |
| rc | Reverse complement of a string using biostrings |
| rep_range | Replication Timing Data as GRanges Object |
| res | res |
| res_annot | res_annot |
| result_collection-class | The Result Collection object that contains modality, input... |
| result_list | Retrieve result_list from a musica object |
| result_model-class | Object that contains results for a single model |
| samp_annot | Get or set sample annotations from a musica object |
| sample_names | Retrieve sample names from a musica object |
| select_genome | Helper function to load common human or mouse genomes |
| signatures | Retrieve signatures from a result_model, result_collection,... |
| subset_musica_by_annotation | Creates a new musica object subsetted to only one value of a... |
| subset_musica_by_counts | Creates a new musica subsetted to only samples with enough... |
| subset_variant_by_type | Subsets a variant table based on Variant Type |
| subset_variants_by_samples | Return sample from musica_variant object |
| table_96 | Generates a 96 motif table based on input counts for plotting |
| tables | Retrieve the list of count_tables from a musica object |
| table_selected | Retrieve table name used for plotting from a result_model... |
| umap | Retrieve umap list from a result_model, result_collection, or... |
| variants | Retrieve variants from a musica object |
