compEpiTools-package    Tools for computational epigenomics
countOverlapsInBins-methods
                        given a query and a subject GRanges returns a
                        matrix of counts of subject in bins of query
distanceFromTSS-methods
                        Returns the GRanges annotated with info about
                        the closer TSS
enhancers-methods       A GRanges method to define enhancers based on
                        H3K4me1 peaks
findLncRNA              Identify putative long non coding RNAs (lncRNA)
getPromoterClass        Determining the CpG promoter class and the
                        average CpG content
GR2fasta-methods        A GRanges method to extract and write to the
                        disk a fasta file containing genomic sequences
                        for the GRanges regions in a genome
GRanges2ucsc-methods    A GRanges method to convert ranges information
                        into UCSC format
GRangesInPromoters-methods
                        Based on a GRanges and a TxDb, subsets the
                        GRanges to those regions overalpping with
                        promoters
GRannotate-methods      Based on a GRanges and a TxDb, returns the
                        GRanges with a series of annotations
GRannotateSimple-methods
                        a GRanges method to split a GRanges in three
                        GRanges: promoter, intragenic and intergenic
GRbaseCoverage-methods
                        Based on a GRanges and a BAM file, returns a
                        list of base coverage vectors for each range
GRcoverage-methods      based on a GRanges and a BAM file, returns the
                        total coverage for each range, or for each bin
                        of the range.
GRcoverageSummit-methods
                        Based on a GRanges and a BAM file, returns a
                        GRanges with the positions of maximum coverage
                        within each range
GRenrichment-methods    Determines the enrichment over a set of genomic
                        regions given two BAM files
GRmidpoint-methods      Returns a GRanges containing the mid point of a
                        GRanges
GRsetwidth-methods      Set the width of a GRanges based on the mid
                        point of each region
heatmapData             Based on a list of GRanges, determine various
                        kind of counts before displaying a heatmap
heatmapPlot             displays the heatmap based on the data from
                        heatmapData
makeGtfFromDb-methods   Utilities to transform a TxDb into a GTF file
matchEnhancers-methods
                        GRanges method to match enhancers with putative
                        targets sites
overlapOfGRanges-methods
                        visualization of GRanges overlap
palette2d               build a two dimensional color palette
plotStallingIndex       Stalling Index plots
simplifyGOterms         simplify a list of GO terms
stallingIndex           returns a list with average read count on TSS,
                        gene body, and stalling index for a number of
                        samples
topGOres                determines GeneOntology (GO) enriched terms for
                        a set of Entrez gene ids
TSS                     based on a TxDb returns a GRanges with the TSS
                        positions for all transcripts
ucsc2GRanges            Convert UCSC-formatted genomic positions into a
                        GRanges
unionMaxScore-methods   GRanges method to perform union of peaks
                        keeping the score of the most significant peak
