Changelog

Log transform for LR analysis

• Fix Log transform for LR analysis Fixed log transformation to normalised counts.

LR analysis and UMAP controls

• Improved LR analysis: rank-aggregate Rank-aggregate support added to logistic regression for improved marker ranking.
• Fix LR results patch Clearer analysis params and timestamps on results; fixed multiple runs for one primary grouping with varied secondary group selection.
• Improved UMAP parameter UI Usability improvements to UMAP parameter controls on the Analyze page.

UMAP parameter exposure

• Improved UMAP parameter exposure Customise UMAP with min_dist and spread on the Analyze page; values appear in analysis info.

CyteType overhaul

• Improved CyteType overhaul Secure report links, better job tracking, deduped per-cell annotations on rerun, and a manual retry when annotation import fails.

CyteType integration

• New CyteType integration AI-powered cell type annotation via CyteType, with study context and report workflow in Explore.
• New Auto-annotation model upgrade Improved automatic cell type detection accuracy and coverage.

Scatter plot legend

• Fix Scatter plot legend Legend correctly excludes cells hidden by category filters when viewing another category.

UMAP scatterplot legend fix

• Fix UMAP scatterplot legend fix Cluster cell counts in the legend no longer include excluded or hidden cells.

Cluster marker p-values

• Improved Cluster marker p-values Markers table now includes per-cluster p-values.

Comparison validation

• Improved Comparison validation Faster, more responsive cell-overlap checks when building comparisons.
• Fix Pseudobulking secondary group Fixed secondary group option when set to "None".

Violin plots and analysis thumbnails

• Fix Violin plot categories Fixed wrong categories in violin plots and related plot rendering.
• Fix Missing thumbnails Fixed missing analysis thumbnails.

Report module reference

Clearer docs for ontology mapping, evidence trails, and review workflows.