A pipeline to analyze photographs of disk diffusion plates. This removes the need to analyze the plates themselves, and thus analysis can be done separate from the assay. Furthermore, diskImageR removes potential researcher bias, by quantitative assessment of drug resistance as the zone diameter at multiple cutoff values of growth inhibition. This method also extends the disk diffusion assay by measuring drug tolerance (in addition to drug resistance) as the fraction of the subpopulation that is able to grow above the resistance point ("FoG"), and drug sensitivity as the rate of change from no growth to full growth ("slope").
|Author||Aleeza Gerstein [aut, cre], Inbal Hecht [ctb]|
|Date of publication||2016-04-03 16:29:24|
|Maintainer||Aleeza Gerstein <email@example.com>|
addType: Add factor column
aggregateData: Averages photographs of the same type
calcMIC: Convert RAD to MIC based on built-in or provided parameters...
createDataframe: Dataframe creation
IJMacro: Run an imageJ analysis macro on the folder that contains the...
maxLik: Maximum Likelihood Inference
oneParamPlot: Used to plot a single parameter
plotRaw: Used to plot the results of the imageJ analysis
readExistingDF: Read in an existing dataframe using the tcltk interface
readInExistingIJ: Used to read in existing imageJ analyses
saveMLParam: Save maximum likelihood output
threeParamPlot: Used to plot the RAD, slope and FoG parameter results
twoParamPlot: Used to plot the RAD and FoG results