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

  • 2026-06-23 · Version 2.2.0 (changelog) Updated mutation-prediction models, added clustered-noise and mitochondrial/contig filtration controls, and improved RNA-feature and PhyloSOLID handling.

  • 2026-06-15 · Version 2.1.2 (changelog) Fixed genotyping to use per-spot cell numbers from the cell_num step output.

  • 2026-06-08 · Version 2.1.1 (changelog) Fixed a PhyloSOLID input formatting issue so the integrated phylogeny step can run successfully.

  • 2026-06-05 · Version 2.1.0 (changelog) Updated the demo package, improved Space Ranger 4.0.1 clustering compatibility, simplified the config templates, and added the integrated PhyloSOLID phylogeny step.

  • 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 Default Step Config
  4. Run the packaged example with Demo
  5. Run your own sample with Quick Start
  6. Use the Step-by-step guide (code-aligned with SpaceTracer/steps) for stage-level details
  7. Review outputs and validation plots in Outputs