Call wide peaks for sequencing data

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Documentation for package ‘NADfinder’ version 1.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
computeLibSizeChrom	Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.
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
IntersectionNotStrict	Count reads overlapping genomic ranges
log2se	calculate the log2 transformed ratios for SummarizedExperiment class
NADfinder	Identify nucleolus-associated domains (NADs) from NAD-seq
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