From: HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
H3K4me3 | |||||||
---|---|---|---|---|---|---|---|
Method (# of peaks) | Peak Finder | MACS | HPeak | Find Peaks | ChIP seeqer | SISSRs | CisGenome |
Peak Finder (28,960) | Â | 84.3 | 99.8 | 100.0 | 98.2 | 98.0 | 99.6 |
MACS (27,568) | Â | Â | 90.6 | 95.4 | 84.8 | 87.7 | 84.8 |
HPeak (41,217) | Â | Â | Â | 99.4 | 100 | 98.9 | 97.1 |
FindPeaks (33,886) | Â | Â | Â | Â | 100 | 99.8 | 100 |
ChIPseeqer (31,773) | Â | Â | Â | Â | Â | 99.0 | 100 |
SISSRs (137,286) | Â | Â | Â | Â | Â | Â | 94.6 |
CisGenome (46,261) | Â | Â | Â | Â | Â | Â | Â |
H3K27me3 | |||||||
Method (# of peaks) | Peak Finder | MACS | HPeak | Find Peaks | ChIP seeqer | SISSRs | CisGenome |
Peak Finder (335) | Â | 44.8 | 99.7 | 100 | 77.3 | 90.4 | 70.9 |
MACS (1,341) | Â | Â | 42.5 | 42.4 | 23.5 | 24.4 | 32.9 |
HPeak (4,858) | Â | Â | Â | 72.1 | 77.7 | 98.2 | 82.0 |
FindPeaks (8,346) | Â | Â | Â | Â | 77.7 | 91.6 | 87.1 |
ChIPseeqer (417) | Â | Â | Â | Â | Â | 58.5 | 75.8 |
SISSRs (2,455) | Â | Â | Â | Â | Â | Â | 25.4 |
CisGenome (437) | Â | Â | Â | Â | Â | Â | Â |