A toolkit for performing KNN-based statistics for flow and mass cytometry data

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Documentation for package ‘Sconify’ version 1.25.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

AddTsne	Add tSNE to your results.
bz.gmcsf.final	Bodenmiller-Zunder GM-CSF post-SCONE final data
bz.gmcsf.final.norm.scale	Bodenmiller-Zunder GM-CSF post-SCONE final data, that's been quantile normalized and z scored.
exist	Random musing
FcsToTibble	Takes a file as input and returns a data frame of cells by features
Fnn	Compute knn using the fnn algorithm
funct.markers	Functional markers from the Wanderlust dataset.
GetKnnDe	Get the KNN density estimaion
GetMarkerNames	Takes in an example file as input and returns all marker names
Impute	Imputes values for all markers (used as input) for each cell
ImputeTesting	Impute testing
input.markers	Input markers for the Wanderlust dataset
LogTransformQ	Log transform the q values
MakeHist	make.hist
MakeKnnList	Make list of cells by features for each KNN member
markers	Markers for the Wanderlust dataset
MeaningOfLife	Meaning of life
MultipleDonorStatistics	Runs a t test on the medians or means of multiple donors for the same condition
ParseMarkers	Parse markers contained in a Sconify-directed marker file
PostProcessing	Post-processing for scone analysks.
ProcessMultipleFiles	Converts multiple files into a concatenated data frame
QCorrectionThresholding	Corrects all p values for multiple hypotheses, sets threshold for which change values should be reported
QuantNormalize	Performs quantile normalization on the data frame (patient) of interest
QuantNormalizeElements	Takes a list of tibbles as input, and performs per-column quantile normalization, then outputs the quantile normalized list
RunStatistics	Performs a series of statistical tests on the batch of cells of interest.
SconeValues	Master function for per-knn statistics functionality, integrating the other non-exported functions within this script.
SplitFile	Runs "process.multiple.files" on a single file, splits it randomly, and presends half of it is "unstim" and half of it is "stim"
StringToNumbers	Transform strings to numbers.
SubsampleAndTsne	Subsample data and run tSNE
TsneVis	Plot a tSNE map colored by a marker of interest
wand.combined	Wanderlust data combined basal and IL7 cells
wand.final	Post-scone output of the "combiend" Wanderlust data.
wand.ideal.k	A named vector to help the user determine the ideal k for the Wanderlust dataset.
wand.il7	Wanderlust IL7 data
wand.scone	Wanderlust scone output