SpaceTracer

SpaceTracer is a computational framework for detecting somatic single-nucleotide variants (SNVs) directly from spatial transcriptomics data and reconstructing cellular lineages within native tissue architecture.

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Release notes

  • 2026-04-30 · Version 2.0.0 (changelog) Added one-command workflow execution, integrated lysis error calculation into the main pipeline, and delivered major runtime performance improvements.

  • 2026-02-25 · Version 1.1.0 Updated genotype calculation, improved random forest features, and added additional filtering steps to improve accuracy.

  • 2025-03-31 · Version 1.0.0 Initial release of SpaceTracer.

Get started

  1. Installation
  2. Resources
  3. Configuration and Config Reference
  4. Run your first sample with Quick Start
  5. Use the Step-by-step guide (code-aligned with SpaceTracer/steps) for stage-level details
  6. Review outputs and validation plots in Outputs