Man pages for jianhong/NADfinder
Call wide peaks for sequencing data
| backgroundCorrection | Correct ratios for background |
| butterFilter | Low pass filter on ratios by butterworth filter |
| callPeaks | Call peaks using transformed, background corrected, and... |
| computeLibSizeChrom | Perform overlap queries between reads and genome by sliding... |
| cumulativePercentage | Plot the cumulative percentage of tag allocation |
| exportSignals | Output signals for visualization |
| getCorrelations | Get correlation coefficinets and p-values between biological... |
| groupZscores | Calculate z-scores for each peak |
| IntersectionNotStrict | Count reads overlapping genomic ranges |
| log2se | calculate the log2 transformed ratios for... |
| NADfinder-package | 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... |
| 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... |
| transformData | transform counts to log2 cpm ratios, log2 ratios or log2 odds... |
| trimPeaks | Trim peaks |
| triplicate.count | Counts data for chromosome 18 for an expriment with... |
| zscoreOverBck | Z-scores over the background |
