Bed2Granges             Read a bed file as Genomic Ranges
CompareBeds2GivenRegions
                        Compare a set of bed files to a provided
                        regions set
CompareMotifs2GivenRegions
                        Comparison motifs locations to a given regions
                        set
DeleteMultipleFiles     Delete a vector of files
DetectBindingSites      Detect binding sites from motif
DetectBindingSitesBed   Detect binding sites from bed motif input
DetectBindingSitesMotif
                        Detect binding sites from sequence motif
                        sequence and mismatchNumber
DetectFdrCutoffBH       FDR cut-off detection Benjamini Hochberg method
Motif2Site              Detect and Recenter binding sites from ChIP-seq
                        experiments
NegativeBinomialTestWithReplicate
                        Negative binomial test of binding using all
                        replicates
combine2Table           Combine all IP and Input count table files
combineMotifFiles       Combine motif bed files into a combined ranges
combineTestResults      Combine count Table and statistics table
compareBedFiless2UserProvidedRegions
                        Compare a set of bed files to a user provided
                        regions set
compareMotifs2UserProvidedRegions
                        Compare a set of motifs to a user provided
                        regions set
computeFoldEnrichment   compute fold enrichment values for an
                        experiment
data                    Synthetic datasets used in the package
decomposeBindingSignal
                        Decompose binding signal among accepted motifs
deriveHeuristicBindingDistribution
                        build heurisitc distribution around the binding
                        sites
findMotifs              Find motif instances with a certain mismatch
                        number
fitKernelDensity        Fit a kernel density distribution to the
                        obersever heuristic distribution
generate1ntBedAlignment
                        Convert bam and bed files to 1 nucleotide bed
motifBindingNegativeBinomialCount
                        Model IP and Input count values with negative
                        Binomal
motifChipCount          count short reads related to each motif for a
                        given ChIPseq file
motifCount              count short reads around motifs for all
                        ChIP-seq experiments
motifTablePreProcess    Process count data and perform negative
                        binomial test
pairwisDifferential     Detect differential motifs
quiet                   Suppress messages generated by in external
                        package
recenterBindingSitesAcrossExperiments
                        Combine binding sites across experiments
removeNonBellShapedMotifs
                        Remove non-bell shpape motifs prior to binding
                        signal decomposition
strongestMotif          Returns the motif with the highest count
