IntersectionNotStrict   Count reads overlapping genomic ranges
NADfinder-package       Identify nucleolus-associated domains (NADs)
                        from NAD-seq
backgroundCorrection    Correct ratios for background
butterFilter            Low pass filter on ratios by butterworth filter
callPeaks               Call peaks using transformed, background
                        corrected, and smoothed ratios with biological
                        replicates
cumulativePercentage    Plot the cumulative percentage of tag
                        allocation
exportSignals           Output signals for visualization
getCorrelations         Get correlation coefficinets and p-values
                        between biological replicates
groupZscores            Calculate z-scores for each peak
log2se                  calculate the log2 transformed ratios for
                        SummarizedExperiment class
peakdet                 Detect peak positions
plotSig                 Plot signals with ideograms
single.count            Counts data for chromosome 18 for an experiment
                        of a single pair of samples
smoothRatiosByChromosome
                        Backgound correction and signal smoothing per
                        chromosome
tileCount               Perform overlap queries between reads and
                        genome by windows
tileCount2              Perform overlap queries between reads and
                        genome by sliding windows Count reads over
                        sliding windows.
transformData           transform counts to log2 cpm ratios, log2
                        ratios or log2 odds ratios
trimPeaks               Trim peaks
triplicate.count        Counts data for chromosome 18 for an expriment
                        with triplicates
zscoreOverBck           Z-scores over the background
