Call wide peaks for sequencing data


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Documentation for package ‘NADfinder’ version 1.6.1

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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
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