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| arrayImage | Function to visualize spatial distribution of raw intensities |
| autocor | Function to compute auto-correlation of probe intensities |
| autocorr | Function to compute auto-correlation of probe intensities |
| autocorrelation | Function to compute auto-correlation of probe intensities |
| chipAlongChrom | Visualize ChIP intensities along the chromosome |
| compute.gc | Compute the GC content of DNA and probe sequences |
| computeRunningMedians | Function to compute running medians on a tiling expression set |
| corPlot | Function to plot correlation of different samples |
| corrPlot | Function to plot correlation of different samples |
| findPeaksOnSmoothed | Find peaks on smoothed ExpressionSet |
| ftr2xys | Convert a NimbleScan ftr-file into a xys-file |
| gccontent | Compute the GC content of DNA and probe sequences |
| image.RGList | Function to visualize spatial distribution of raw intensities |
| peak | Class peak - A list holding ChIP-chip peak characteristics |
| peak-class | Class peak - A list holding ChIP-chip peak characteristics |
| peakByThreshold | Function to identify peaks based on thresholds |
| peakList | Class peak - A list holding ChIP-chip peak characteristics |
| peakList-class | Class peak - A list holding ChIP-chip peak characteristics |
| peakPlot | Plot identified peaks |
| plot.autocor.result | Plots auto-correlation of probe intensities |
| plot.peak | Plot identified peaks |
| plotAutocor | Plots auto-correlation of probe intensities |
| plotPeak | Plot identified peaks |
| preprocess | Preprocess Nimblegen Raw Intensities |
| print.peak | Class peak - A list holding ChIP-chip peak characteristics |
| readNimblegen | Function to read in Nimblegen Intensity Text Files |
| relatePeaks | Relate found peaks to genomic features |
| sliding.quantile | Compute quantile of scores in a sliding window |
| slidingquantile | Compute quantile of scores in a sliding window |