omicverse-single-cell-cytotrace2

To predict single-cell developmental potency from an AnnData object, apply OmicVerse CytoTRACE2 to estimate differentiation potential. The tool scores mouse or human scRNA-seq data and validates outputs like CytoTRACE2_Score and CytoTRACE2_Potency.

CytoTRACE2 potency scoring estimates the developmental potential of individual cells from scRNA-seq data. You need it when identifying high-potency populations in mouse or human datasets to understand cellular differentiation hierarchies.

Yes, CytoTRACE2 supports preprocessing mode, HVG strategy selection, batch sizing, and parallelization control for scRNA-seq datasets. These operational guardrails ensure reliable inference on large mouse or human AnnData objects.

To validate CytoTRACE2 outputs, check for expected columns including CytoTRACE2_Score, CytoTRACE2_Potency, CytoTRACE2_Relative, and preKNN variants. You can then optionally overlay these validated scores onto an existing UMAP embedding.

Yes, you can use scanpy and anndata workflows to run CytoTRACE2 on human scRNA-seq data. The Skill requires scanpy and omicverse dependencies, allowing you to specify the human organism setting during inference.

A key limitation is that pretrained weight staging requires correct species selection between mouse and human. If the input matrix needs normalization, you must properly configure the preprocessing mode and HVG strategy before inference.