# Call wide peaks for sequencing data

## Documentation for package ‘NADfinder’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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