Coordinate              Loading, manipulating, and analyzing coordinate
                        data.
EXPLORE                 Function generates various exploratory
                        analyses.
Kmer_Table              A R6 class wrapper for data.table
NCBI_Genome             Class constructor - build NCBI Genome object
SCORE                   Calculate susceptibility scores for k-mers in
                        case and control regions.
STUDY_ACROSS_POPULATIONS
                        Study k-mer composition of selected COSMIC
                        causal cancer genes across human populations
                        worldwide.
STUDY_ACROSS_SPECIES    Study k-mer composition across species.
STUDY_CANCER_GENES      Study k-mer composition of causal cancer genes
                        from COSMIC Cancer Gene Census (CGC) database.
STUDY_GENIC_ELEMENTS    Study k-mer composition across species.
UCSC_Genome             Class constructor - build Genome object
addAlphaCol             Add transparency to color.
bedToCoor               Convert a BED file to chromosome-separated csv
                        files.
buildControl            Build control regions
buildKmerTable          Count k-mers from given sequence(s) and build a
                        data.table of k-mer counts.
buildMidPatternKmerTable
                        Count k-mers with specified middle pattern from
                        given sequence(s) and build a data.table of
                        k-mer counts.
buildRESTurl            Function constructs a URL for a REST API call
                        by appending query parameters.
buildRangedKmerTable    Count kmers from a sequence in given ranges and
                        build a data.table of k-mer counts.
calKmerSkew             Function calculates the skew of k-mers based on
                        their occurrence in positive and negative
                        strands.
calPWM                  Calculate position weight matrix of overlapping
                        sequences. Simulation of human population is
                        based on single nucleotide variation.
catHeader               Function prints a given message in a formatted
                        header with borders.
countBaseComposition    Function performs an analysis of base
                        composition including sequence frequency, PWM
                        calculations, and G/C content at various window
                        sizes.
countChoppedKmers       Function chops k-mers within specified ranges
                        of a sequence and counts them. It uses either a
                        substring method or functionalities from the
                        Biostrings package.
countDistribution       Function performs an analysis of the
                        distribution of genomic cases.
countKmers              Count k-mers from string(s) using a simple hash
                        table.
countMidPatternContext2
                        Locate a middle sequence pattern and count its
                        sequence context.
countMidPatternKmers    Count Relevant K-mers with Specified Middle
                        Pattern from Sequence String(s)
countPointContext2      Ccount sequence context of given point
                        positions.
countRangedKmers        Count k-mers in given ranges of a sequence.
countRevCompKmers       Count reverse complement sequence from its
                        opposite strand. Build for k-mer table
                        generated from initKmerTable function but
                        applicable to others with the same format.
countSlidingWindow      Count sequence content in a sliding window of a
                        sequence.
countSlidingWindow2     Count sequence content in a sliding window of a
                        sequence.
count_substring_fixed   Count sequence content in a given sequence.
count_substring_regex   Count sequence content in a given sequence.
downloadNCBIGenomes     Function downloads genome fasta files from the
                        NCBI FTP database. Users can provide either
                        organism names or an assembly summary data
                        table.
downloadUCSCgenome      Function downloads chromosome-separated fasta
                        genome sequences from the UCSC database. Users
                        can specify a genome name, an output folder,
                        and a specific chromosome or chromosomes.
                        There's an option to choose the download method
                        as well.
example_genome_coor     Example genome coordinate file
example_kmeRtone_score
                        Example 2-mer enrichment/depletion scores
extractKmers            Extract k-mers from a given Coordinate object
                        and Genome objects
generateGenicElementCoor
                        Function processes UCSC genePred tables to
                        generate coordinates for various genic elements
                        like introns, exons, CDS, UTRs, and upstream
                        and downstream regions. It handles these
                        coordinates with consideration for strand
                        sensitivity and genome information.
generateIntergenicCoor
                        Resolve and generate genic element coordinates
                        from UCSC genePred table.
getCOSMICauthURL        Get COSMIC authenticated URL.
getCOSMICcancerGeneCensus
                        Get Cancer Gene Census (CGC) from COSMIC
                        database.
getCOSMIClatestVersion
                        Function retrieves the latest version
                        information of the COSMIC database and the
                        associated genome version by scraping data from
                        the COSMIC website.
getCOSMICmutantExport   Function downloads the latest Cosmic Mutant
                        Export data from the COSMIC database. It
                        requires the user to be registered with COSMIC
                        for non-commercial use. The function constructs
                        the URL for the latest mutant export file,
                        authenticates the URL, and then downloads the
                        data.
getEnsemblData          A generic function to get Ensembl data
                        persistently from a URL. This is an internal
                        function used by other getEnsemblXXX functions.
getEnsemblRegionFeatures
                        Get features of a given region.
getEnsemblVariantFeatures
                        Get features of given variant IDs.
getEnsemblVariantFeatures_serial
                        Get features of given variant IDs.
getGnomADvariants       Get gnomAD VCF file using tabix.
getICTVvirusMetadataResource
                        Get Virus Metadata Resource (VMR) from
                        International Committee on Taxonomy of Viruses
                        (ICTV)
getNCBIassemblySummary
                        Get NCBI assembly summary.
getScores               Function calculates scores for k-mers based on
                        case and control k-mer counts.
getUCSCgenePredTable    Retrieve Gene Prediction Table from UCSC for a
                        Given Genome
getVCFmetainfo          Read VCF metainfo file using tabix.
initKmerTable           Initialise k-mer table with all possible k-mers
kmeRtone                kmeRtone all-in-one user interface
loadCoordinate          Build Coordinate object.
loadGenome              Build Genome object.
loadGenomicContents     Function calculates various genomic content
                        metrics based on the provided genome object.
mapKmers                Map k-mers of a given sequence and coordinate
mergeCoordinate         Merge overlapping or continuous regions.
mixColors               Mix color
partitionCoordinate     Partition overlapping or continuous regions.
persistentDownload      Download file until successful
readBED                 Read a BED file. One-based indexing is
                        enforced.
readFASTA               Read FASTA files.
readVCF                 Read VCF file using tabix.
readVCF2                Read VCF file using tabix.
removeRegion            Remove overlapping region in coordinate
                        'data.table'.
reverseComplement       Get reverse complement sequence of DNA
scoreKmers              Function calculates the Z-score for each k-mer
                        based on the observed case counts and expected
                        case counts under the null hypothesis.
selectGenomesForCrossSpeciesStudy
                        Select genomes for cross-species studies.
selectRepresentativeFromASM
                        Select the best representative species from the
                        NCBI assembly summary.
simulatePopulation      Simulate a population given ranges of
                        chromosome sequence to mutate.
splitFASTA              Split a FASTA file by header.
system3                 A system2 wrapper. If anything happen, just
                        give me error!
trimCoordinate          Trim out-of-bound coordinates
writeBED                Write a BED file. Zero-based indexing is
                        enforced.
writeFASTA              Write FASTA files.
writeVCF                Write VCF file and compress using bgzip.
