Changelog

Source: NEWS.md

CHANGES IN VERSION 1.0.0

• Initial release of the scDiagnostics package.

CHANGES IN VERSION 1.4.0

• 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.

CHANGES IN VERSION 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