NEWS

scDiagnostics 1.6.0

Renamed gene shift function for consistency (previously calculateTopLoadingGeneShifts())
Added gene specification parameter to calculateGeneShifts()
Improved calculateGeneShifts() function, plot method, and color scheme

Add functionality to process SCE objects for PCA computation via the new processPCA() function.
Add functionality to downsample SCE objects for diagnostic functions.
Add new diagnostic functions (calculateTopLoadingGeneShifts(), compareMarkers() and calculateMMDPValue()).
Add graph integration diagnostic function in replacement of nearest neighbor diagnostic, calculateGraphIntegration().
Improve regressPC() function and plot method, which can now also regress against cell types and batches.
Improve normalization for plotMarkerExpression() diagnostic function.
Improve user control and options for plot methods.
Update vignettes to reflect all new changes.