addDiffStatus           Add a status column
as_tibble               Convert to a tibble
bestOverlap             Find the best overlap between GRanges
centrePeaks             Re-estimate peak centres from coverage
chopMC                  Keep unique ranges and collapse mcols
collapseGenes           Collapse a vector of gene names
colToRanges             Coerce a column to a GRanges object
cytobands               Cytogenetic bands
defineRegions           Define Genomic Regions Based on Gene
                        Annotations
defineSeqinfo           Use package data to define a Seqinfo object
distinctMC              Keep distinct ranges and mcols
dualFilter              Apply two filters to sliding windows
ex_datasets             Datasets for an example region
fitAssayDiff            Detect Differential ChIP Signal
fixed_width_datasets    Datasets for the Fixed-Width Vignette
getProfileData          Get Profile Data surrounding specified ranges
grlToSE                 Set columns from a GRangesList as Assays in a
                        SummarizedExperiment
importPeaks             Import peaks
makeConsensus           Make a set of consensus peaks
mapByFeature            Map Genomic Ranges to genes using defined
                        features
mapGrlCols              Collapse a GRangesList adding multiple columns
                        from each element
mergeByCol              Merge sliding windows using a specified column
mergeByHMP              Merge Sliding Windows using the Harmonic Mean P
mergeBySig              Merge overlapping ranges based on p-values
partitionRanges         Partition a set of Genomic Ranges
plotAssayDensities      Plot Densities for any assay within a
                        SummarizedExperiment
plotAssayHeatmap        Draw a heatmap from a single
                        SummarizedExperiment assay
plotAssayPCA            Plot PCA For any assay within a
                        SummarizedExperiment
plotAssayRle            Plot RLE for a given assay within a
                        SummarizedExperiment
plotGrlCol              Draw a plot from a GRangesList column
plotHFGC                Plot a Genomic Region showing HiC, Features,
                        Genes and Coverage
plotOverlaps            Plot Overlaps Between List Elements
plotPairwise            Plot Pairwise Values from a GRangeList
plotPie                 Draw Pie Graphs based on one or more columns
plotProfileHeatmap      Draw a coverage Profile Heatmap
plotSplitDonut          Draw Two-Level Donut Charts
propOverlap             Find the proportions of an overlapping range
reduceMC                Reduce ranges retaining mcols
setoptsMC               Perform set operations retaining mcols
stitchRanges            Stitch Ranges within a given distance
voomWeightsFromCPM      Estimate voom precision weights directly From
                        CPM values
