AnnotateDBSVCF          Add sequence context and transcript information
                        to an in-memory DBS VCF
AnnotateIDVCF           Add sequence context and transcript information
                        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
ConvertCatalogToSigProfilerFormat
                        Covert an ICAMS Catalog to SigProfiler format
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
IsICAMSCatalog          Check whether an R object contains one of the
                        ICAMS catalog classes
MutectVCFFilesToCatalog
                        *[Deprecated, use VCFsToCatalogs(variant.caller
                        = "mutect") instead]* Create SBS, DBS and Indel
                        catalogs from Mutect VCF files
MutectVCFFilesToCatalogAndPlotToPdf
                        *[Deprecated, use
                        VCFsToCatalogsAndPlotToPdf(variant.caller =
                        "mutect") instead]* Create SBS, DBS and Indel
                        catalogs from Mutect VCF files and plot them to
                        PDF
MutectVCFFilesToZipFile
                        *[Deprecated, use VCFsToZipFile(variant.caller
                        = "mutect") instead]* 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
                        *[Deprecated, use
                        ReadAndSplitVCFs(variant.caller = "mutect")
                        instead]* Read and split Mutect VCF files
ReadAndSplitStrelkaSBSVCFs
                        *[Deprecated, use
                        ReadAndSplitVCFs(variant.caller = "strelka")
                        instead]* Read and split Strelka SBS VCF files
ReadAndSplitVCFs        Read and split VCF files
ReadCatalog             Read catalog
ReadStrelkaIDVCFs       *[Deprecated, use
                        ReadAndSplitVCFs(variant.caller = "strelka")
                        instead]* Read Strelka ID (small insertions and
                        deletions) VCF files
ReadVCFs                Read VCF files
SimpleReadVCF           Read a VCF file into a data frame with minimal
                        processing.
SplitListOfVCFs         Split each VCF into SBS, DBS, and ID VCFs (plus
                        VCF-like data frame with left-over rows)
StrelkaIDVCFFilesToCatalog
                        *[Deprecated, use VCFsToCatalogs(variant.caller
                        = "strelka") instead]* Create ID (small
                        insertions and deletions) catalog from Strelka
                        ID VCF files
StrelkaIDVCFFilesToCatalogAndPlotToPdf
                        *[Deprecated, use
                        VCFsToCatalogsAndPlotToPdf(variant.caller =
                        "strelka") instead]* Create ID (small
                        insertions and deletions) catalog from Strelka
                        ID VCF files and plot them to PDF
StrelkaIDVCFFilesToZipFile
                        *[Deprecated, use VCFsToZipFile(variant.caller
                        = "strelka") instead]* Create a zip file which
                        contains ID (small insertions and deletions)
                        catalog and plot PDF from Strelka ID VCF files
StrelkaSBSVCFFilesToCatalog
                        *[Deprecated, use VCFsToCatalogs(variant.caller
                        = "strelka") instead]* Create SBS and DBS
                        catalogs from Strelka SBS VCF files
StrelkaSBSVCFFilesToCatalogAndPlotToPdf
                        *[Deprecated, use
                        VCFsToCatalogsAndPlotToPdf(variant.caller =
                        "strelka") instead]* Create SBS and DBS
                        catalogs from Strelka SBS VCF files and plot
                        them to PDF
StrelkaSBSVCFFilesToZipFile
                        *[Deprecated, use VCFsToZipFile(variant.caller
                        = "strelka") instead]* 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 insertions and deletions)
                        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'
