AnnotateDBSVCF          Add sequence context and transcript information
                        to an in-memory DBS VCF
AnnotateIDVCF           Add sequence context to an in-memory ID
                        (insertion/deletion) VCF, and confirm that they
                        match the given reference genome
AnnotateSBSVCF          Add sequence context and transcript information
                        to an in-memory SBS VCF
Canonicalize1Del        Given a deletion and its sequence context,
                        categorize it
CatalogRowOrder         Standard order of row names in a catalog
CollapseCatalog         "Collapse" a catalog
FindDelMH               Return the length of microhomology at a
                        deletion
FindMaxRepeatDel        Return the number of repeat units in which a
                        deletion is embedded
GeneExpressionData      Example gene expression data from two cell
                        lines
GetVAF                  Extract the VAFs (variant allele frequencies)
                        and read depth information from a VCF file
ICAMS                   ICAMS: In-depth Characterization and Analysis
                        of Mutational Signatures
MutectVCFFilesToCatalog
                        Create SBS, DBS and Indel catalogs from Mutect
                        VCF files
MutectVCFFilesToCatalogAndPlotToPdf
                        Create SBS, DBS and Indel catalogs from Mutect
                        VCF files and plot them to PDF
MutectVCFFilesToZipFile
                        Create a zip file which contains catalogs and
                        plot PDFs from Mutect VCF files
PlotCatalog             Plot *one* spectrum or signature
PlotCatalogToPdf        Plot catalog to a PDF file
PlotTransBiasGeneExp    Plot transcription strand bias with respect to
                        gene expression values
PlotTransBiasGeneExpToPdf
                        Plot transcription strand bias with respect to
                        gene expression values to a PDF file
ReadAndSplitMutectVCFs
                        Read and split Mutect VCF files
ReadAndSplitStrelkaSBSVCFs
                        Read and split Strelka SBS VCF files
ReadAndSplitVCFs        Read and split VCF files
ReadCatalog             Read catalog
ReadStrelkaIDVCFs       Read Strelka ID (small insertion and deletion)
                        VCF files
StrelkaIDVCFFilesToCatalog
                        Create ID (small insertion and deletion)
                        catalog from Strelka ID VCF files
StrelkaIDVCFFilesToCatalogAndPlotToPdf
                        Create ID (small insertion and deletion)
                        catalog from Strelka ID VCF files and plot them
                        to PDF
StrelkaIDVCFFilesToZipFile
                        Create a zip file which contains ID (small
                        insertion and deletion) catalog and plot PDF
                        from Strelka ID VCF files
StrelkaSBSVCFFilesToCatalog
                        Create SBS and DBS catalogs from Strelka SBS
                        VCF files
StrelkaSBSVCFFilesToCatalogAndPlotToPdf
                        Create SBS and DBS catalogs from Strelka SBS
                        VCF files and plot them to PDF
StrelkaSBSVCFFilesToZipFile
                        Create a zip file which contains catalogs and
                        plot PDFs from Strelka SBS VCF files
TranscriptRanges        Transcript ranges data
TransformCatalog        Transform between counts and density spectrum
                        catalogs and counts and density signature
                        catalogs
VCFsToCatalogs          Create SBS, DBS and Indel catalogs from VCFs
VCFsToCatalogsAndPlotToPdf
                        Create SBS, DBS and Indel catalogs from VCFs
                        and plot them to PDF
VCFsToDBSCatalogs       Create DBS catalogs from VCFs
VCFsToIDCatalogs        Create ID (small insertion and deletion)
                        catalog from ID VCFs
VCFsToSBSCatalogs       Create SBS catalogs from SBS VCFs
VCFsToZipFile           Create a zip file which contains catalogs and
                        plot PDFs from VCFs
WriteCatalog            Write a catalog
all.abundance           K-mer abundances
as.catalog              Create a catalog from a 'matrix', 'data.frame',
                        or 'vector'
revc                    Reverse complement every string in 'string.vec'
