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 |