The back end files for the Scotty app. Check ReadMe for version issues.
Matlab
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README.md
ReadMe.pdf
ScottyFiles.zip
clusterSamples.m
fitVariance.m
getCumProbLocation.m
getDispersionAllComparisons.m
getLineMarkers.m
getMuSigmaLognormal.m
getNormalizedSamples.m
getOptimizationByBudget.m
getOptimizationByGoals.m
getOptimizationCharts.m
getParamsVariance.m
getPowerByReadDepth.m
getPowerByReadDepthNoPoisson.m
getPowerPlot.m
getPowerPlotSingleFC.m
getPowerTTest.m
getPowerTTestLogged.m
getProbSequencedMonteCarlo.m
getProbSequencedMonteCarloByReads.m
getProbabilitiesFromFit.m
getPwrBias.m
getRarefactionPlot.m
getReadDepthsRun.m
getReadsRequiredPerSample.m
getSequenceDepthParameters.m
getSlope.m
getTotalPower.m
moneyscale.m
optimizeByGoals.m
printResultFile.m
scottyEstimate.m
scottyPlotScatter.m
scottyPlotScatterComparingSamples.m
scottyReadDataFile.m
testVarFit.m

README.md

Scotty

These are the files that power the backend of the Scotty web app available at scotty.genetics.utah.edu/

These files were written using an older version of Matlab. At some point Matlab depricated one of the functions used which will cause running errors on newer versions (Matlab 2013+) of Matlab.

To use these functions on newer versions of Matlab where it says:

RandStream.setDefaultStream(s);

you have to change it to

RandStream.setGlobalStream(s);

These are located in the following lines:

getProbabilitiesFromFit Line 23

getProbSequencedMonteCarloByReads Line 7

License: Anyone can use Scotty. Ask Gabor Marth if you want to do something besides use it.