asExprSet               converts a Ringo MAList into an ExpressionSet
autocor                 Function to compute auto-correlation of probe
                        intensities
cher-class              Class "cher" - ChIP-enriched region
cherByThreshold         Function to identify chers based on thresholds
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
computeSlidingT         Function to compute sliding T statistics on a
                        tiling expression set
corPlot                 Function to plot correlation of different
                        samples
features2Probes         Function for mapping genomic features to probes
findChersOnSmoothed     Find ChIP-enriched regions on smoothed
                        ExpressionSet
ftr2xys                 Convert a NimbleScan ftr-file into a xys-file
getFeats                Utility function to extract all features from a
                        cherList
image.RGList            Function to visualize spatial distribution of
                        raw intensities
plot.autocor.result     Plots auto-correlation of probe intensities
plot.cher               Plot identified Chers
posToProbeAnno          Function for creating a probeAnno environment
preprocess              Preprocess Nimblegen Raw Intensities
probeAnno-class         Class "probeAnno"
readNimblegen           Function to read in Nimblegen Intensity Text
                        Files
regionOverlap           Function to compute overlap of genomic regions
relateChers             Relate found Chers to genomic features
sliding.meansd          Compute mean and standard deviation of scores
                        in a sliding window
sliding.quantile        Compute quantile of scores in a sliding window
upperBoundNull          function to estimate upper limit of null
                        distribution
