| callMethylation | callMethylation |
| extractPatterns | extractPatterns |
| generateAmpliconReport | generateBedReport |
| generateBedEcdf | generateBedEcdf |
| generateBedReport | generateBedReport |
| generateCaptureReport | generateBedReport |
| generateCytosineReport | generateCytosineReport |
| generateMhlReport | generateMhlReport |
| generateVcfReport | generateVcfReport |
| preprocessBam | preprocessBam |
| preprocessGenome | preprocessGenome |
| simulateBam | simulateBam |