.checkCool              Check for .(m)cool file and contents
.checkCoolErrors        Error checking function for .(m)cool files
.coolAutoResolution     Determine best resolution for size of region
                        for .(m)cool files
.coolRegion             Add (alt)chromstart and (alt)chromend for NULL
                        (alt)chrom region of .(m)cool files
.pullBinChunks          Read in data for a bin chunk
annoDomains             Annotate domains in a Hi-C plot
annoGenomeLabel         Annotate genomic coordinates along the x or
                        y-axis of a plot
annoHeatmapLegend       Add a color scale legend for heatmap-style
                        plots
annoHighlight           Annotates a highlight box around a specified
                        genomic region of a plot
annoPixels              Annotate pixels in a Hi-C plot
annoSegments            Annotates a line segment within a plot
annoText                Annotates text within a plot
annoXaxis               Add an x-axis to a plot
annoYaxis               Add a y-axis to a plot
annoZoomLines           Annotates zoom lines for a specified genomic
                        region of a plot
assembly                Make a 'assembly' object for alternate TxDb,
                        OrgDb,and BSgenome genomic annotation packages
c                       Combine multiple pgParams objects into a vector
calcSignalRange         Calculate a score range for multiple signals
colorby                 Handle plotgardener color scaling parameters
defaultPackages         Display the default genomic annotation packages
                        associated with a genome build
genomes                 Display the included available default genome
                        assemblies
mapColors               Maps a numeric or character vector to a color
                        palette and returns the vector of colors
pageCreate              Create a page for a plotgardener layout
pageGuideHide           Remove guides from a plotgardener page
pageGuideHorizontal     Draw a horizontal guideline at a specified
                        y-coordinate on a plotgardener page
pageGuideShow           Reshow guides drawn with 'pageCreate',
                        'pageGuideHorizontal', and 'pageGuideVertical'
pageGuideVertical       Draw a vertical guideline at a specified
                        x-coordinate on a plotgardener page
pageLayoutCol           Generate column positions for a number of plot
                        elements with a specified width and space
                        between them
pageLayoutRow           Generate row positions for a number of plot
                        elements with a specified height and space
                        between them
pagePlotPlace           Place a plot that has been previously created
                        but not drawn
pagePlotRemove          Remove plotgardener plots and annotations
pgParams                pgParams: plotgardener parameters object
plotCircle              Plot a circle within a plotgardener layout
plotGG                  Plot a ggplot2 plot, gtable, or grob object in
                        a plotgardener layout
plotGenes               Plot a gene track for a specified genomic
                        region
plotGenomeLabel         Plot genomic coordinates along the x or y-axis
                        of a plotgardener plot
plotHicRectangle        Plot a triangular Hi-C interaction matrix in a
                        rectangular format
plotHicSquare           Plot a Hi-C interaction matrix in a square
                        format
plotHicTriangle         Plot a Hi-C interaction matrix in a triangular
                        format
plotIdeogram            Plot a chromosome ideogram with or without
                        cytobands
plotLegend              Plot a legend
plotManhattan           Plot a Manhattan plot
plotMultiSignal         Plot multiple signal tracks in line with each
                        other
plotPairs               Plot paired-end genomic range elements
plotPairsArches         Plot paired-end genomic range data in an arch
                        style
plotPolygon             Plot a polygon within a plotgardener layout
plotRanges              Plot genomic range elements in a pileup or
                        collapsed format
plotRaster              Plot a raster object within a plotgardener
                        layout
plotRect                Plot a rectangle within a plotgardener layout
plotSegments            Draw a line segment within a plotgardener
                        layout
plotSignal              Plot any kind of signal track data for a single
                        chromosome
plotText                Plot text within a plotgardener layout
plotTranscripts         Plot gene transcripts in a pileup style for a
                        single chromosome
plotgardener            plotgardener: Coordinate-based Genomic
                        Visualization Package for R
readBigwig              Read a bigWig file and return it as a data
                        frame
readCool                Read a .(m)cool file and return Hi-C data as a
                        dataframe
readCoolBpResolutions   Read basepair resolutions from an .(m)cool file
readCoolChroms          Read chromosomes included in .(m)cool files
readCoolNorms           Read normalizations included in .(m)cool files
readHic                 Read a .hic file and return Hi-C data as a
                        dataframe
