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Changelog

Source: NEWS.md

scGate 1.7.2

CRAN release: 2025-07-23

Breaking Changes

  • Removed UCell dependency - Integrated UCell scoring algorithm directly into scGate
  • This resolves the SeuratObject V5 Layers() dependency issue

Seurat Compatibility

  • Seurat V4 Priority: All functions now prioritize Seurat V4 compatibility (tested with 4.4.0)
  • Seurat V5 Compatible: Also works with Seurat V5 through compatibility layer
  • Uses Seurat::GetAssayData() instead of SeuratObject::Layers() for V4 compatibility

New Internal Functions

Other Improvements

  • Cross-platform compatibility: replaced system("rm -r") with unlink() for Windows support
  • Numerical stability: improved MCC calculation to handle edge cases (log(0), integer overflow)
  • Performance optimization: vectorized operations (rowSums, pmax, max.col)
  • Code quality: fixed potential bugs with 1:length() loops, improved parameter validation

Dependency Changes

  • Removed: UCell (>= 2.6.0)
  • Added: BiocNeighbors, Matrix

Maintainer

scGate 1.7.0

CRAN release: 2025-04-24

  • Update maintainer emails
  • Bug fixes

scGate 1.6.2

CRAN release: 2024-04-23

  • Enable parallelization over a list of scGate models (in multi-classifier mode)
  • Fix bug on parallelization when specifying BPPARAM
  • Added cell ontology links for controlled cell type dictionary
  • Update accessor functions for compatibility with Seurat v5

scGate 1.4.0

  • Use function SmoothKNN() from the UCell package for nearest neighbor smoothing of signature scores
  • Clean up code for CRAN submission

scGate 1.2.0

  • Simultaneously evaluate multiple gating models, given as a list to model parameter. This returns individual gatings as well as a combined cell type annotation from all the models (scGate_multi metadata column), and allows running scGate as a multi-class classifier and annotate cell types in a dataset.
  • New reduction parameter: this i) Allows nearest-neighbor smoothing on an existing dimensionality reduction (e.g. “pca” or “harmony”) and ii) Can significantly speed up computation time and annotation of integrated objects