diskImageR: A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

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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 <gerst035@umn.edu>
License
GPL-3
Version
1.0.0

View on CRAN

Man pages

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

Files in this package

diskImageR
diskImageR/inst
diskImageR/inst/walkthrough.R
diskImageR/inst/diskImageR_vignette.html
diskImageR/inst/IJ_diskImageR.ijm
diskImageR/inst/knownMIC-RAD.csv
diskImageR/NAMESPACE
diskImageR/R
diskImageR/R/saveMLParam.R
diskImageR/R/readExistingDF.R
diskImageR/R/mle.R
diskImageR/R/IJMacro.R
diskImageR/R/addType.R
diskImageR/R/aggregateData.R
diskImageR/R/createDataframe.R
diskImageR/R/readExistingIJ.R
diskImageR/R/maxLik.R
diskImageR/R/plotRaw.R
diskImageR/R/twoParamPlot.R
diskImageR/R/calcMIC.R
diskImageR/R/oneParamPlot.R
diskImageR/R/threeParamPlot.R
diskImageR/README.md
diskImageR/MD5
diskImageR/DESCRIPTION
diskImageR/man
diskImageR/man/plotRaw.Rd
diskImageR/man/addType.Rd
diskImageR/man/readExistingDF.Rd
diskImageR/man/threeParamPlot.Rd
diskImageR/man/twoParamPlot.Rd
diskImageR/man/maxLik.Rd
diskImageR/man/readInExistingIJ.Rd
diskImageR/man/createDataframe.Rd
diskImageR/man/saveMLParam.Rd
diskImageR/man/calcMIC.Rd
diskImageR/man/oneParamPlot.Rd
diskImageR/man/IJMacro.Rd
diskImageR/man/aggregateData.Rd