| callPeak | Call peaks |
| CMHpeaks | differential binding analysis by Cochran-Mantel-Haenszel Test |
| count5end | count reads by regions |
| countTable | Counting reads in features |
| DBFpeaks | differential binding analysis |
| DEpeaks | differential binding analysis |
| diffPeaks-package | Quantifying Differential Features |
| FTpeaks | differential binding analysis by Fisher's exact test |
| IntersectionNotStrict | Count reads overlapping genomic ranges |
| isCountTable | is output of countTable |
| mergePeaks | Merge BED files |
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