Using Mass Cytometry for Differential Abundance Analyses

Documentation for package ‘cydar’ version 1.17.0

cbind-method	CyData class and methods
cellAssignments	CyData class and methods
cellInformation	CyData class and methods
cellIntensities	CyData class and methods
countCells	Count cells in high-dimensional space
createColorBar	Create a color bar
CyData	CyData class and methods
CyData-class	CyData class and methods
dnaGate	Gate events based on DNA channels
expandRadius	Expand the hypersphere radius
findFirstSphere	Identifies the first non-redundant hyperspheres
getCenterCell	CyData class and methods
intensities	CyData class and methods
intensityRanges	Define intensity ranges
interpretSpheres	Interactive interpretation of hyperspheres
labelSpheres	Label unannotated hyperspheres
markernames	CyData class and methods
markernames-method	CyData class and methods
medIntensities	Compute median marker intensities
multiIntHist	multiIntHist
neighborDistances	Compute distances to neighbors
normalizeBatch	Normalize intensities across batches
outlierGate	Create an outlier gate
pickBestMarkers	Pick best markers
plotSphereIntensity	Plot cell or hypersphere data
plotSphereLogFC	Plot changes in hypersphere abundance
poolCells	Pool cells for pre-processing
prepareCellData	Prepare mass cytometry data
show-method	CyData class and methods
spatialFDR	Compute the spatial FDR
[-method	CyData class and methods
[<--method	CyData class and methods