Seurat 5.6 Beta: Core Workflows Rewritten with Coding Agents
arjunrajlab · x · 2026-08-25
Seurat v5.6 public beta introduces major improvements for speed, memory, and scalability.
- Methodology: The team used coding agents to rewrite core workflows, migrating steps from R to C++ and optimizing code.
- Performance: Huge improvements observed, with some cases seeing >10x speedups while maintaining identical outputs.
- Scope: Updated functions include NormalizeData, FindVariableFeatures, ScaleData, SCTransform, RunPCA, FindNeighbors, FindClusters, RunUMAP, and FindMarkers.
- Technical Gains: Speedups primarily come from software engineering, moving computations to C++, and multithreading.
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