| colonyzer.read | Reads raw cell density timecourse data from Colonyzer output files |
| correlationReport | Correlation Report |
| dtl | Culture Doubling Time for Generalised Logistic Function (as a function of time t) |
| fitnessReport | Fitness Report |
| getDeadLocations | Find dead cultures in SGA plates (1536 format), and report their location in spotted plates (384 format). |
| Glogist | Generalised Logistic growth curve model |
| loapproxfun | Model free growth curve approximation |
| logist | Logistic growth curve model |
| makeFitness | Generate QFA fitnesses |
| makeVisTool | Making the visualisation tool |
| mdp | Maximum Doubling Potential (MDP) for Generalised Logistic Function |
| mdr | Maximum Doubling Rate (MDR) for Generalised Logistic Function |
| mdrmdp | Fitness value for Generalised Logistic Function |
| normalisePlates | Normalising culture fitness by plate |
| pgis | Calculate strength and significance of genetic interaction. |
| plateBoxplots | Plate Boxplots |
| qfa.epi | Finds genetic interaction strengths and p-values |
| qfa.epiplot | Makes an epistasis plot from the full results of qfa.epi |
| qfa.fit | Growth curve modelling |
| qfa.plot | Plots fitted model and data for all the colonies in results of qfa.fit |
| report.epi | Normalising culture fitness by plate |
| rod.read | Reading of ROD raw timecourse data. Deprecated. |
| rod.write | Writes a synthetic ROD-like output file to hard-drive. Deprecated. |
| showDemo | Show Demo |
| visToolDemo | Interactive fitness plots from Addinal et al. 2011 PLoS Genetics |