# Using Mass Cytometry for Differential Abundance Analyses

## Documentation for package ‘cydar’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cbind-method | CyData class and methods
cellAssignments | CyData class and methods
cellAssignments-method | 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-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
intensities-method | 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
plotCellIntensity | Plot cell or hypersphere data
plotCellLogFC | Plot changes in hypersphere abundance
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