autocor                 Function to compute auto-correlation of probe
                        intensities
chipAlongChrom          Visualize ChIP intensities along the chromosome
computeRunningMedians   Function to compute running medians on a tiling
                        expression set
corPlot                 Function to plot correlation of different
                        samples
findPeaksOnSmoothed     Find peaks on smoothed ExpressionSet
ftr2xys                 Convert a NimbleScan ftr-file into a xys-file
image.RGList            Function to visualize spatial distribution of
                        raw intensities
peak                    Class peak - A list holding ChIP-chip peak
                        characteristics
peakByThreshold         Function to identify peaks based on thresholds
plot.autocor.result     Plots auto-correlation of probe intensities
plot.peak               Plot identified peaks
preprocess              Preprocess Nimblegen Raw Intensities
readNimblegen           Function to read in Nimblegen Intensity Text
                        Files
relatePeaks             Relate found peaks to genomic features
sliding.median          Compute median score over a running window
sliding.quantile        Compute quantile of scores in a sliding window
