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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

CHANGES IN VERSION 1.8.0

  • Added calculateReconstructionError() to detect out-of-distribution anomalies using cell-type-specific PCA reconstruction errors.
  • Added plot.calculateReconstructionErrorObject() featuring robust visualization options (violin, boxplot, ridge, and ComplexHeatmap).
  • Upgraded detectAnomaly() to resolve the curse of dimensionality by allowing Isolation Forests to run on the union of query and reference Highly Variable Genes (via n_hvgs) when pc_subset = NULL.
  • Improved anomaly detection by switching default thresholding to a dynamic, data-driven Median Absolute Deviation method (threshold_method = "MAD", mad_multiplier = 2) across relevant functions.