Man pages for qfa
Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces
| checkTarg | checkTarg |
| colonyzer.read | Reads raw cell density timecourse data from Colonyzer output... |
| correlationReport | Correlation Report |
| datafit | Fitting generalised logistic model to growth data by least... |
| dtl | Culture Doubling Time for Generalised Logistic Function (as a... |
| fitnessReport | Fitness Report |
| getDeadLocations | Find dead cultures in SGA plates (1536 format), and report... |
| getMissingGenotypes | getMissingGenotypes |
| getMissingSGA | getMissingSGA |
| getNeighbours | getNeighbours |
| Glogist | Generalised Logistic growth curve model |
| growthcurve | Wrapper function for generating QFA generalised logistic... |
| iRVisDemo | Interactive fitness plots from Addinal et al. 2011 PLoS... |
| loapproxfun | Model free growth curve approximation |
| logist | Logistic growth curve model |
| makeBoundsQFA | Generate generalised logistic parameter bounds for QFA |
| makeFitness | Generate QFA fitnesses |
| mdp | Maximum Doubling Potential (MDP) for Generalised Logistic... |
| mdr | Maximum Doubling Rate (MDR) for Generalised Logistic Function |
| mdrmdp | Fitness value for Generalised Logistic Function |
| normalisePlates | Normalising culture fitness by plate |
| numericalfitness | Numerical fitness estimates from timecourse data |
| numerical_r | Generates numerical fitnesses from experimental growth curve... |
| 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-Internal | Internal qfa Functions |
| qfa.plot | Plots fitted model and data for all the colonies in results... |
| readMer | readMer |
| readSGD | readSGD |
| 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.... |
| showDemo | Show Demo |
| visTool | Making the visualisation tool |
