Man pages for MarioniLab/cydar
Using Mass Cytometry for Differential Abundance Analyses
| countCells | Count cells in high-dimensional space |
| createColorBar | Create a color bar |
| CyData | CyData class and methods |
| dnaGate | Gate events based on DNA channels |
| expandRadius | Expand the hypersphere radius |
| findFirstSphere | Identifies the first non-redundant hyperspheres |
| intensityRanges | Define intensity ranges |
| interpretSpheres | Interactive interpretation of hyperspheres |
| labelSpheres | Label unannotated hyperspheres |
| 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 |
| spatialFDR | Compute the spatial FDR |
