Release notes#

Release 1.0.3 (released January 20, 2026)#

PIASOmarkerDB client and API

  • New Features

    • PIASOmarkerDB Python Client: This release introduces the PIASOmarkerDB Python client, providing programmatic access to PIASOmarkerDB - our comprehensive database of cell type marker genes with standardized specificity scores across studies, tissues, species and conditions.

  • Key Features

    • Query marker genes by gene, cell type, study, species, and tissue

    • Analyze gene lists to infer cell types from marker genes

    • COSG integration for automated cell type annotation workflows

    • Study filtering to restrict analysis to specific reference studies

    • Download markers directly to CSV files

  • Documentation

Release 1.0.2 (released November 22, 2025)#

SCALAR, StitchSpace & Parallel Stability

  • New Features

    • Ligand-Receptor Analysis: Added piaso.tl.runSCALAR for single-cell L-R inference.

    • Dataset Integration: Added piaso.tl.stitchSpace for integrating datasets.

    • Preprocessing: Added utility for 2D coordinate rotation in piaso.pp.

  • Visualization

    • SCALAR Plots: Added piaso.pl.plotLigandReceptorInteraction and piaso.pl.plotLigandReceptorLollipop.

    • Metrics: Added piaso.pl.plotConfusionMatrix.

  • Critical Stability

    • Fixed “Unsafe Fork” Crash: Switched ProcessPoolExecutor to use the ‘spawn’ start method. This resolves Terminating: fork() called from a process already using GNU OpenMP errors on Linux/macOS.

    • Strict Seeding: random_seed is now enforced across internal steps (Neighbors, Leiden).

    • Race Condition Resolved: Fixed a logic error in parallel functions where results were processed by completion order rather than batch order. Results are now explicitly sorted.

  • Compatibility & Maintenance

    • Updated for Pandas 2.1+ (applymap -> map) and fixed Scanpy/AnnData warnings.

Thank you for your feedback and support!

Release 1.0.1 (released March 18, 2025)#

Bug Fixes and Enhancements

  • Enhanced tl.score: Improved gene set scoring functionality with P value for each cell

  • Enhanced tl.infog: Improved INFOG normalization with more user-friendly data manipulation and clearer variable naming

  • Enhanced pl.plot_embeddings_split: Added global legend option for simplified visualization

  • New Feature: Introduced tl.predictCellTypeByMarker function for marker gene-based cell type prediction

  • Improved API: Refined function interfaces for better usability and consistency

  • Dependency Update: Added COSG v1.0.3 to fix errors and improve verbosity control

This release focuses on improving stability and user experience while maintaining full compatibility with existing workflows.

Thank you for your feedback and support!

Release 1.0.0 (released February 24, 2025)#

The first official release of PIASO