add_flank_to_variants   Uses a genome object to find context and add it
                        to the variant table
add_result              Load an external model into a musica object
annotate_replication_strand
                        Add replication strand annotation to SBS
                        variants based on bedgraph file
annotate_transcript_strand
                        Add transcript strand annotation to SBS
                        variants (defined in genes only)
annotate_variant_length
                        Adds an annotation to the input musica's
                        variant table with length of each variant
annotate_variant_type   Annotate variants with variant type ("SBS",
                        "INS", "DEl", "DBS")
auto_predict_grid       Automatic filtering of signatures for exposure
                        prediction gridded across specific annotation
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 discovery/prediction
combine_predict_grid    Combine signatures and exposures of different
                        models. Exposure values are zero for samples in
                        an annotation where that signature was not
                        predicted
compare_cosmic_v2       Compare a result object to COSMIC V2 SBS
                        Signatures (combination whole-exome and
                        whole-genome)
compare_cosmic_v3       Compare a result object to COSMIC V3
                        Signatures; Select exome or genome for SBS and
                        only genome for DBS or Indel classes
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 signatures
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 descriptions that we generated
                        by provided and by user functions. These are
                        used to discover and infer signatures and
                        exposures.
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_umap             Create a UMAP from a model result
credible_intervals      Retrieve credible_intervals from a
                        result_model, result_collection, or musica
                        object
dbs_musica              dbs_musica
discover_signatures     Discover mutational signatures
drop_annotation         Drops a column from the variant table that the
                        user no longer needs
exposure_differential_analysis
                        Compare exposures of annotated samples
exposures               Retrieve exposures from a result_model,
                        result_collection, or musica object
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 range of k
get_count_table         Retrieve count_table matrix from count_table
                        object
get_modality            Retrieve a specific modality entry from a
                        musica or result_collection object
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 object
indel_musica            indel_musica
k_select                Plots for helping decide number of clusters
metrics                 Retrieve metrics from a result_model,
                        result_collection, or musica object
modality                Retrieve modality from a result_model,
                        result_collection, or musica object
model_id                Retrieve model_id from a result_model,
                        result_collection, or musica object
musica                  musica
musica-class            The primary object that contains variants,
                        count_tables, and samples annotations
musica_annot            musica_annot
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,
                        result_collection, or musica object
other_parameters        Retrieve other_parameters from a result_model,
                        result_collection, or musica object
parameter               Retrieve parameter from a musica or
                        result_collection object
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 signatures
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 parameters, prior
                        hyperparameters
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, or musica object
subset_musica_by_annotation
                        Creates a new musica object subsetted to only
                        one value of a sample annotation
subset_musica_by_counts
                        Creates a new musica subsetted to only samples
                        with enough variants
subset_variant_by_type
                        Subsets a variant table based on Variant Type
subset_variants_by_samples
                        Return sample from musica_variant object
table_selected          Retrieve table name used for plotting from a
                        result_model object
tables                  Retrieve the list of count_tables from a musica
                        object
umap                    Retrieve umap list from a result_model,
                        result_collection, or musica object
variants                Retrieve variants from a musica object
