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| alignAdjust | Custom Alignability Track Generation |
| basealigncount | Get SBC (basecount) for Mapped Sample Reads |
| basecountimport | Import SBC (basecounts) Given Coordinate File |
| buildwindowdata | Build Datasets for Mixture Regression Model |
| covariateselect | Determine Best Sets of Covariates to Model Each Component |
| covariateselect | Determine Best Sets of Covariates to Model Each Component |
| getrefinedpeaks | Refine Peak Boundaries from Collapsed Significant Regions |
| getsigwindows | Determine Significantly Enriched Windows |
| peakbound | Refine Peak Boundaries from SBC Collapsed Significant Regions |
| run.zinba | Run Analysis pipeline |
| summary.zinba | Printing summary of the ZINBA peak finding software |
| twobittofa | Convert Fasta Formatted Files From .2bit |
| zinba | ZINBA convenience function |