| binHist | Histogram Breakpoints |
| binInsert | Insert Locations |
| binInsertHist | Insert Locations Quickly |
| checkFormat | Checks the Format of Annotation and Insertions |
| delta0 | Number of New Knockouts |
| eMult | Expected Value of the Occupancy Distribution |
| etDelta | Number of New ORF Knockouts |
| fCumul | Parametric Function for the Cumulative Occupancy Distribution |
| fFit | Parametric Fit for the Cumulative Occupancy Distribution |
| loadAnnotation | Loads Annotation File |
| loadInsertions | Load Genome Annotation File |
| occup2Negenes | Convert Occupancy Format to Negenes |
| sampleAnnotation | Annotation for a Hypothetical Prokayote |
| sampleInsertions | Insertions for a Hypothetical Clonal Library |
| unbiasB0 | Unbiased Estimator of the Number of Non-essential ORFs |
| unbiasDelta0 | Unbiased Number of New Knockouts |
| varMult | Variance of the Occupancy Distribution |