MutationalPatterns      MutationalPatterns: an integrative R package
                        for studying patterns in base substitution
                        catalogues
binomial_test           Binomial test for enrichment or depletion
                        testing
cluster_signatures      Signature clustering function
cos_sim                 Cosine similarity function
cos_sim_matrix          Compute all pairwise cosine similarities
                        between mutational profiles/signatures
enrichment_depletion_test
                        Test for enrichment or depletion of mutations
                        in genomic regions
explained_by_signatures
                        This function has been renamed to
                        'cos_sim_matrix'.
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.
genomic_distribution    Find overlaps between mutations and a genomic
                        region.
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        This function has been removed.  Use
                        'mut_context' instead.
mutation_types          This function has been renamed.  Use 'mut_type'
                        instead.
mutations_from_vcf      Retrieve base substitutions from vcf
plot_192_profile        Plot 192 trinucleotide profile
plot_96_profile         Plot 96 trinucleotide profile
plot_compare_profiles   Compare two 96 mutation profiles
plot_contribution       Plot signature contribution barplot
plot_contribution_heatmap
                        Plot signature contribution heatmap
plot_cosine_heatmap     Plot cosine similarity heatmap
plot_enrichment_depletion
                        Plot enrichment/depletion of mutations in
                        genomic regions
plot_rainfall           Plot genomic rainfall
plot_signature_strand_bias
                        Plot signature strand bias
plot_spectrum           Plot point mutation spectrum
plot_strand             Plot strand per base substitution type
plot_strand_bias        Plot strand bias per base substitution type per
                        group
read_vcfs_as_granges    Read VCF files into a GRangesList
strand_bias_test        Significance test for strand asymmetry
strand_from_vcf         This function has been renamed. Use
                        'mut_strand' instead.
strand_occurrences      Count occurrences per base substitution type
                        and strand
type_context            Retrieve context of base substitution types
