omicverse-single-cell-cytotrace2

What problem does it solve?

This Skill automates running pretrained CytoTRACE2 on single-cell AnnData to produce robust developmental potency scores and related annotations, removing manual notebook steps and fragile ad-hoc commands.

Core Features & Use Cases

• Prepare and validate an AnnData object with optional preprocessing and HVG selection before inference.
• Stage or verify pretrained CytoTRACE2 weights, run batched prediction and KNN smoothing, and write five potency columns into adata.obs for downstream analysis.
• Expose branching for species selection (mouse/human), batch and smoothing chunking, and parallelization controls to support smoke tests and production runs.
• Use case: convert a CytoTRACE2 tutorial notebook into a reusable invocation that scores 100+ cells reliably and optionally overlays results on existing embeddings.

Quick Start

Run CytoTRACE2 on my AnnData to produce CytoTRACE2_Score and CytoTRACE2_Potency using species mouse with staged model weights.