# Call wide peaks for sequencing data

## Documentation for package ‘NADfinder’ version 1.2.0

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

## Help Pages

NADfinder-package | Call peaks for nucleolar-associated domains (NADs) sequencing data
backgroundCorrection | Correct ratios for background
butterFilter | Low pass filter on ratios by butterworth filter
callPeaks | call peaks for ratios of repeats
countByOverlaps | Count overlapping genomic ranges
cumulativePercentage | Plot the cumulative percentage tag allocation in sample
exportSignals | output signals to file
getCorrelations | get correlations for replicates
groupZscores | Calculate z-scores for each peak
log2ratio | calculate the log2 transformed ratios
log2se | calculate the log2 transformed ratios for SummarizedExperiment class
NADfinder | Call peaks for nucleolar-associated domains (NADs) sequencing data
peakdet | Detect peak positions
plotSig | plot signals with ideograms
single.count | counts data for single experiment of chromosome 18
smoothRatiosByChromosome | smooth the ratios by chromosome
tileCount | Perform overlap queries between reads and genome by windows
trimPeaks | Trim peaks
triplicates.counts | counts data for triplicates of chromosome 18
zscoreOverBck | Z-scores over the background