Changes in version 1.12.0 o prepareCellData() now returns a List rather than a half-complete CyData object. o expandRadius() and neighborDistances() work explicitly on the List produced by prepareCellData(). o countCells() will compute weighted-median intensities for unused markers as well. Minor bugfix to avoid stochastic results due to numerical imprecision when computing medians. o intensities() has a new mode= argument to return intensities for unused markers. Changes in version 1.10.0 o Removed deprecated plotCell* functions. Changes in version 1.8.0 o Modified the plotSphere*() functions for more flexibility in colour choice. o Added fix.zero= option in normalizeBatch() for range-based normalization. Changes in version 1.6.0 o Restructured the CyData class for simplicity and internal fields. o Deprecated plotCell* functions, renamed them to plotSphere*. o Added the createColorBar() convenience function. o Removed the diffIntDist() function. o Restored option for quantile normalization in normalizeBatch(). Switched to deterministic algorithm for sampling when mode="warp". Changes in version 1.4.0 o Bug fix to interpreSpheres() when making additional plots. o Switched to custom colour calculation in plotCellIntensity(). Changes in version 1.2.0 o Added labelSpheres() function for labelling unannotated hyperspheres. o Exported multiIntHist() for plotting multiple intensity histograms. o Slight fix to spatialFDR(), which now computes the correct n-th nearest neighbour. Changes in version 1.0.0 o New package cydar, for detecting differential abundance in mass cytometry data.