| bindWidth | ChIP-seq Binding Width And Peak Window Size Estimation |
| gcapcPeaks | GC Effects Aware Peak Calling |
| gcEffects | ChIP-seq GC Effects Estimation |
| peaksCAT | CATplot of Peaks |
| read5endCoverage | Reads Coverage Using 5-end Base |
| refinePeaks | Refine Peaks with GC Effects |
| refineSites | Adjust ChIP-seq Read Count Table |
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