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 |