Man pages for tjburns08/Sconify
A toolkit for performing KNN-based statistics for flow and mass cytometry data

AddTsneAdd tSNE to your results.
bz.gmcsf.finalBodenmiller-Zunder GM-CSF post-SCONE final data
bz.gmcsf.final.norm.scaleBodenmiller-Zunder GM-CSF post-SCONE final data, that's been...
existRandom musing
FcsToTibbleTakes a file as input and returns a data frame of cells by...
FnnCompute knn using the fnn algorithm
funct.markersFunctional markers from the Wanderlust dataset.
GetKnnDeGet the KNN density estimaion
GetMarkerNamesTakes in an example file as input and returns all marker...
ImputeImputes values for all markers (used as input) for each cell
ImputeTestingImpute testing
input.markersInput markers for the Wanderlust dataset
LogTransformQLog transform the q values
MakeHistmake.hist
MakeKnnListMake list of cells by features for each KNN member
markersMarkers for the Wanderlust dataset
MeaningOfLifeMeaning of life
MultipleDonorStatisticsRuns a t test on the medians or means of multiple donors for...
ParseMarkersParse markers contained in a Sconify-directed marker file
PostProcessingPost-processing for scone analysks.
ProcessMultipleFilesConverts multiple files into a concatenated data frame
QCorrectionThresholdingCorrects all p values for multiple hypotheses, sets threshold...
QuantNormalizePerforms quantile normalization on the data frame (patient)...
QuantNormalizeElementsTakes a list of tibbles as input, and performs per-column...
RunStatisticsPerforms a series of statistical tests on the batch of cells...
SconeValuesMaster function for per-knn statistics functionality,...
SplitFileRuns "process.multiple.files" on a single file, splits it...
StringToNumbersTransform strings to numbers.
SubsampleAndTsneSubsample data and run tSNE
TsneVisPlot a tSNE map colored by a marker of interest
wand.combinedWanderlust data combined basal and IL7 cells
wand.finalPost-scone output of the "combiend" Wanderlust data.
wand.ideal.kA named vector to help the user determine the ideal k for the...
wand.il7Wanderlust IL7 data
wand.sconeWanderlust scone output
tjburns08/Sconify documentation built on April 23, 2018, 7:15 p.m.