chipseqFilter           Filtering ChIP-seq reads
coverageplot            Plot coverage on a small interval.
cstest                  A test ChIP-Seq dataset
diffPeakSummary         A function to identify and produce summary
                        statistics for differentially expressed peaks.
estimate.mean.fraglen   Estimate summaries of the distribution of
                        fragment lengths in a short-read experiment.
                        The methods are designed for ChIP-Seq
                        experiments and may not work well in data
                        without peaks.
islandDepthPlot         Plot island depth distribution
laneSubsample           Subsample short read alignment locations
peakCutoff              Calculate a peak cutoff
peakSummary-methods     Summarizing peak sets
subsetSummary           Compute summaries for cumulative subsets of a
                        short-read data set.