BS_org_map              BS genome organism dictionary
annotate_cpg_sites      Annotate CpG sites
bmd_proast              BMD modeling using PROAST
calculate_mf            Calculate mutation frequency
characterize_variants   Characterize Variants
check_required_columns
                        Check that all required columns are present
                        before proceeding with the function
classify_variation      classify_variation
cleveland_plot          Cleveland Plot
cluster_spectra         Hierarchical Clustering
context_list            A list of reference contexts at different
                        resolutions
denominator_dict        Values used for denominators in frequency
                        calculations
f.plot.gui              Manages plotting for PROAST
f.plot.result           Plot the PROAST results
f.proast                Run dose-response modeling using PROAST.
filter_mut              Filter your mutation data
find_BS_genome          Find the appropriate BS genome for the
                        specified organism and genome.
get_binom_ci            Add binomial confidence intervals to mutation
                        frequencies.
get_cpg_mutations       Get mutations at CpG sites.
get_cpg_regions         Get the coordinates of the CpG sites within
                        your genomic regions
get_ref_of_mut          A utility function that will return the
                        reference context of a mutation
get_seq                 Get sequence of genomic target regions
import_mut_data         Import tabular mutation data
import_regions_metadata
                        Join Regions Metadata
import_sample_data      Join Sample Metadata
import_vcf_data         Import a VCF file
load_regions_file       Imports the regions file
model_mf                Perform linear modelling on mutation frequency
                        for given fixed and random effects
op                      Dictionary of column name synonyms for required
                        mutation data columns
plot_bubbles            Generate Bubble Plots
plot_ci                 plot_ci
plot_lollipop           Plot recurrent mutations in a lollipop plot
                        using ggplot2
plot_mean_mf            Plot the Mean Mutatation Frequency
plot_mf                 Plot the Mutation Frequency
plot_model_mf           Plot your mf model
plot_radar              Create a radar plot
plot_spectra            Plot spectra
plot_trinucleotide      Plot the trinucleotide spectrum
plot_trinucleotide_heatmap
                        Create a heatmap plot of mutation subtype
                        proportions.
populate_sequence_context
                        Populate Sequence context
print_ascii_art         This function prints ASCII art when the package
                        is loaded
rename_columns          Map column names of mutation data to default
                        column names. A utility function that renames
                        columns of mutation data to default columns
                        names.
render_report           Read configuration file and render R Markdown
                        document
reverseComplement       Get the reverse complement of a DNA or RNA
                        sequence.
setup_mutseqr_python    Set up Python environment for MutSeqR
sidak                   Correct p-values for multiple comparisons
signature_fitting       Run COSMIC signatures comparison using
                        SigProfilerAssignment
spectra_comparison      Compare the overall mutation spectra between
                        groups
subtype_dict            Subtype Resolution Dictionary
subtype_list            A comprehensive list of mutation subtypes at
                        different resolutions
vcf_sample_fix          Retrieve the sample column from VCF files
write_excel             Write results to Excel tables
write_mutation_calling_file
                        Write the mutation calling file to input into
                        the SigProfiler Assignment web application.
write_mutational_matrix
                        Write a Mutational Matrix to input into the
                        sigprofiler web application
write_reference_fasta   Write FASTA file of reference sequences.
write_vcf_from_mut      Write mutation_data to a VCF file
