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omicverse-single-cell-cytotrace2

Predict developmental potency scores from single-cell AnnData matrices using pretrained CytoTRACE2.

13|2|Updated Apr 5, 2026
Search Tags:#parallelization#batching#preprocessing#single-cell#anndata#cytotrace2#potency
One-click install
npx skills add https://github.com/Starlitnightly/omicverse-skills --skill omicverse-single-cell-cytotrace2
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: omicverse-single-cell-cytotrace2
Source: https://github.com/Starlitnightly/omicverse-skills/tree/main/src/omicverse_skills/skills/single-cell-cytotrace2
Command: npx skills add https://github.com/Starlitnightly/omicverse-skills --skill omicverse-single-cell-cytotrace2

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires omicverse, scanpy, and includes scripts (resource) and references (resource) and assets (resource) components.

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.

Frequently Asked Questions about omicverse-single-cell-cytotrace2

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I predict single-cell developmental potency scores from an AnnData matrix?▼

Predict single-cell developmental potency scores by running pretrained CytoTRACE2 on your scRNA-seq AnnData matrix, which applies batched prediction and KNN smoothing to write potency columns into adata.obs for downstream analysis.

What is CytoTRACE2 developmental potency prediction and when is it needed?▼

CytoTRACE2 developmental potency prediction uses pretrained models to score single-cell scRNA-seq data, needed when you want to estimate differentiation states and robust potency annotations without manual notebook steps.

Can I use scanpy AnnData with mouse and human scRNA-seq datasets for CytoTRACE2 potency scoring?▼

Yes, scanpy AnnData works with CytoTRACE2 potency scoring for both mouse and human scRNA-seq datasets, requiring explicit species selection and appropriate gene-symbol casing before running batched predictions.

Do I need to preprocess single-cell AnnData and select HVGs before running developmental potency prediction?▼

Preprocessing single-cell AnnData and selecting highly variable genes (HVGs) are optional steps before developmental potency prediction, allowing you to prepare and validate data before staging pretrained model weights for inference.

How do I handle large scRNA-seq datasets when running CytoTRACE2 potency prediction?▼

Handle large scRNA-seq datasets during CytoTRACE2 potency prediction by configuring batch_size, smoothing chunking, and parallelization settings to support both smoke tests and production runs reliably.

What are the limitations of using pretrained CytoTRACE2 weights for single-cell potency scoring?▼

Limitations of using pretrained CytoTRACE2 weights include requiring staged model weights, explicit species specification, and appropriate gene-symbol casing, meaning incorrect input formatting or missing weights will halt potency prediction.

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