.requireAndReturn       Checks to make sure a package object is
                        installed, and if so, returns it. If the
                        library is not installed, it issues a warning
                        and returns NULL.
.validateInputs         Checks class of the list of variables. To be
                        used in functions
BSdtToGRanges           Converts a list of data.tables (From
                        BSreadbeds) into GRanges.
GenomicDistributions-package
                        Produces summaries and plots of features
                        distributed across genomes
TSS_hg19                hg19 TSS locations
binBSGenome             Bins a BSgenome object.
binChroms               Naively splits a chromosome into bins
binRegion               Divide regions into roughly equal bins
calcChromBins           Calculates the distribution of a query set over
                        the genome
calcChromBinsRef        Returns the distribution of query over a
                        reference assembly Given a query set of
                        elements (a GRanges object) and a reference
                        assembly (*e.g. 'hg38'), this will aggregate
                        and count the distribution of the query
                        elements across bins of the reference genome.
                        This is a helper function to create features
                        for common genomes. It is a wrapper of
                        'calcChromBins', which is more general.
calcChromBinsRefSlow    Returns the distribution of query over a
                        reference assembly Given a query set of
                        elements (a GRanges object) and a reference
                        assembly (*e.g. 'hg38'), this will aggregate
                        and count the distribution of the query
                        elements across bins of the reference genome.
                        This is a helper function to create features
                        for common genomes. It is a wrapper of
                        'calcChromBins', which is more general.
calcCumulativePartitions
                        Calculates the cumulative distribution of
                        overlaps between query and arbitrary genomic
                        partitions
calcCumulativePartitionsRef
                        Calculates the cumulative distribution of
                        overlaps for a query set to a reference
                        assembly
calcDinuclFreq          Calculate Dinuclotide content over genomic
                        ranges
calcDinuclFreqRef       Calculate dinucleotide content over genomic
                        ranges
calcExpectedPartitions
                        Calculates expected partiton overlap based on
                        contribution of each feature (partition) to
                        genome size. Expected and observed overlaps are
                        then compared.
calcExpectedPartitionsRef
                        Calculates the distribution of observed versus
                        expected overlaps for a query set to a
                        reference assembly
calcFeatureDist         Find the distance to the nearest genomic
                        feature
calcFeatureDistRefTSS   Calculates the distribution of distances from a
                        query set to closest TSS
calcGCContent           Calculate GC content over genomic ranges
calcGCContentRef        Calculate GC content over genomic ranges
calcNearestNeighbors    Group regions from the same chromosome together
                        and compute the distance of a region to its
                        nearest neighbor.  Distances are then lumped
                        into a numeric vector.
calcNeighborDist        Group regions from the same chromosome together
                        and calculate the distances of a region to its
                        upstream and downstream neighboring regions.
                        Distances are then lumped into a numeric
                        vector.
calcPartitions          Calculates the distribution of overlaps between
                        query and arbitrary genomic partitions
calcPartitionsRef       Calculates the distribution of overlaps for a
                        query set to a reference assembly
calcSummarySignal       The function calcSummarySignal takes the input
                        BED file(s) in form of GRanges or GRangesList
                        object, overlaps it with all defined open
                        chromatin regions across conditions (e.g. cell
                        types) and returns a matrix, where each row is
                        the input genomic region (if overlap was
                        found), each column is a condition, and the
                        value is a meam signal from regions where
                        overlap was found.
calcWidth               Calculate the widths of regions
cellTypeMetadata        Table the maps cell types to tissues and groups
chromSizes_hg19         hg19 chromosome sizes
dtToGr                  Converts a data.table (DT) object to a
                        GenomicRanges (GR) object. Tries to be
                        intelligent, guessing chr and start, but you
                        have to supply end or other columns if you want
                        them to be carried into the GR.
dtToGrInternal          Two utility functions for converting
                        data.tables into GRanges objects
exampleOpenSignalMatrix_hg19
                        A dataset containing a subset of open chromatin
                        regions across all cell types defined by ENCODE
                        for Homo Sapiens hg19
geneModels_hg19         hg38 gene models
genomePartitionList     Create a basic genome partition list of genes,
                        exons, introns, UTRs, and intergenic
getChromSizes           Returns built-in chrom sizes for a given
                        reference assembly
getChromSizesFromFasta
                        Get gene models from a remote or local FASTA
                        file
getGeneModels           Returns built-in gene models for a given
                        reference assembly
getGeneModelsFromGTF    Get gene models from a remote or local GTF file
getGenomeBins           Returns bins used in 'calcChromBins' function
                        Given a named vector of chromosome sizes, the
                        function returns GRangesList object with bins
                        for each chromosome.
getReferenceData        Get reference data for a specified assembly
getTssFromGTF           Get transcription start sites (TSSs) from a
                        remote or local GTF file
grToDt                  Convert a GenomicRanges into a data.table.
labelCuts               Creates labels based on a discretization
                        definition.
loadBSgenome            Loads BSgenome objects from UCSC-style
                        character vectors.
loadEnsDb               Load selected EnsDb library
neighbordt              Internal helper function to calculate distance
                        between neighboring regions.
nlist                   Nathan's magical named list function. This
                        function is a drop-in replacement for the base
                        list() function, which automatically names your
                        list according to the names of the variables
                        used to construct it. It seamlessly handles
                        lists with some names and others absent, not
                        overwriting specified names while naming any
                        unnamed parameters. Took me awhile to figure
                        this out.
plotChromBins           Plot distribution over chromosomes
plotCumulativePartitions
                        Plot the cumulative distribution of regions in
                        features
plotDinuclFreq          Plot dinuclotide content within region set(s)
plotExpectedPartitions
                        Produces a barplot showing how query regions of
                        interest are distributed relative to the
                        expected distribution across a given partition
                        list
plotFeatureDist         Plots a histogram of distances to genomic
                        features
plotGCContent           Plots a density distribution of GC vectors Give
                        results from the 'calcGCContent' function, this
                        will produce a density plot
plotNeighborDist        Plot the distances from regions to their
                        upstream/downstream neighbors or nearest
                        neighbors. Distances can be passed as either
                        raw bp or corrected for the number of regions
                        (log10(obs/exp)), but this has to be specified
                        in the function parameters.
plotPartitions          Produces a barplot showing how query regions of
                        interest are distributed across a given
                        partition list
plotQTHist              Plot quantile-trimmed histogram
plotSummarySignal       The function plotSummarySignal visualizes the
                        signalSummaryMatrix obtained from
                        'calcSummarySignal'.
retrieveFile            Read local or remote file
setB_100                Example BED file read with rtracklayer::import
splitDataTable          Efficiently split a data.table by a column in
                        the table
theme_blank_facet_label
                        Clear ggplot face label.
vistaEnhancers          Example BED file read with rtracklayer::import
