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
TSS                     based on a TxDb returns a GRanges with the TSS
                        positions for all transcripts
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
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
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
