MutationalPatterns      MutationalPatterns: an integrative R package
                        for studying patterns in base substitution
                        catalogues
bin_mutation_density    Bin the genome based on mutation density
binomial_test           Binomial test for enrichment or depletion
                        testing
calculate_lesion_segregation
                        Calculate the amount of lesion segregation for
                        a GRangesList or GRanges object.
cluster_signatures      Signature clustering function
context_potential_damage_analysis
                        Potential damage analysis for the supplied
                        mutational contexts
convert_sigs_to_ref     Convert tissue specific signature exposures to
                        reference
cos_sim                 Cosine similarity function
cos_sim_matrix          Compute all pairwise cosine similarities
                        between mutational profiles/signatures
count_dbs_contexts      Count DBS contexts
count_indel_contexts    Count indel contexts
count_mbs_contexts      Count MBS variants grouped by length.
enrichment_depletion_test
                        Test for enrichment or depletion of mutations
                        in genomic regions
extract_signatures      Extract mutational signatures from 96 mutation
                        matrix using NMF
fit_to_signatures       Find optimal nonnegative linear combination of
                        mutation signatures to reconstruct the mutation
                        matrix.
fit_to_signatures_bootstrapped
                        Fit mutational signatures to a mutation matrix
                        with bootstrapping
fit_to_signatures_strict
                        Fit mutational signatures to a mutation matrix
                        with less overfitting
genomic_distribution    Find overlaps between mutations and a genomic
                        region.
get_dbs_context         Get DBS context
get_indel_context       Get indel contexts
get_known_signatures    Get known signatures
get_mut_type            Get variants with mut_type from GRanges
lengthen_mut_matrix     Lengthen mutation matrix
merge_signatures        Merge signatures based on cosine similarity
mut_192_occurrences     Count 192 trinucleotide mutation occurrences
mut_96_occurrences      Count 96 trinucleotide mutation occurrences
mut_context             Retrieve context of base substitutions
mut_matrix              Make mutation count matrix of 96 trinucleotides
mut_matrix_stranded     Make mutation count matrix of 96 trinucleotides
                        with strand information
mut_strand              Find strand of mutations
mut_type                Retrieve base substitution types from a VCF
                        object
mut_type_occurrences    Count the occurrences of each base substitution
                        type
mutation_context        Defunct functions in package
                        'MutationalPattern'
mutations_from_vcf      Retrieve base substitutions from vcf
plot_192_profile        Plot 192 trinucleotide profile
plot_96_profile         Plot 96 trinucleotide profile
plot_bootstrapped_contribution
                        Plot the bootstrapped signature contributions
plot_compare_dbs        Compare two dbs mutation profiles
plot_compare_indels     Compare two indel mutation profiles
plot_compare_mbs        Compare two mbs mutation profiles
plot_compare_profiles   Compare two 96 mutation profiles
plot_contribution       Plot signature contribution barplot
plot_contribution_heatmap
                        Plot signature contribution heatmap
plot_correlation_bootstrap
                        Plots the correlation between bootstrapped
                        signature contributions
plot_cosine_heatmap     Plot cosine similarity heatmap
plot_dbs_contexts       Plot the DBS contexts
plot_enrichment_depletion
                        Plot enrichment/depletion of mutations in
                        genomic regions
plot_indel_contexts     Plot the indel contexts
plot_lesion_segregation
                        Plot the strands of variants to show lesion
                        segregation
plot_main_dbs_contexts
                        Plot the main DBS contexts
plot_main_indel_contexts
                        Plot the main indel contexts
plot_mbs_contexts       Plot the MBS contexts
plot_original_vs_reconstructed
                        Plot the similarity between a mutation matrix
                        and its reconstructed profile
plot_profile_heatmap    Plot a mutation matrix as a heatmap
plot_profile_region     Plot 96 trinucleotide profile per subgroup
plot_rainfall           Plot genomic rainfall
plot_river              Plot a riverplot
plot_signature_strand_bias
                        Plot signature strand bias
plot_spectrum           Plot point mutation spectrum
plot_spectrum_region    Plot point mutation spectrum per genomic region
plot_strand             Plot strand per base substitution type
plot_strand_bias        Plot strand bias per base substitution type per
                        group
pool_mut_mat            Pool multiple samples from a mutation matrix
                        together
read_vcfs_as_granges    Read VCF files into a GRangesList
rename_nmf_signatures   Rename NMF signatures based on previously
                        defined signatures
signature_potential_damage_analysis
                        Potential damage analysis for the supplied
                        mutational signatures
split_muts_region       Split GRangesList or GRanges based on a list of
                        regions.
strand_bias_test        Significance test for strand asymmetry
strand_occurrences      Count occurrences per base substitution type
                        and strand
type_context            Retrieve context of base substitution types
