Author

Zhao Li

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Review Open access Aug 2026

scATrans: annotating single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA

What scATrans adds is the inference layer single-cell reanalysis actually needs—DE-defined membership, gene-structure correction, a capture-regime reliability pre-flight, induction-matched testing, and a permutation-calibrated program score—so that confident calls are reserved for where the data support them: gene prog...

Zhao Li, A. James, Sheng-Xuan Li · bioRxiv · 0 citations

Open access Aug 2026

scFair: Geometry-Aware Gene Budgets and Same-Rank Extension for Highly Variable Gene Selection

Background Highly variable gene (HVG) selection begins almost every single-cell RNA-seq analysis. While ranking formulas have been compared extensively, the integer gene budget at which any ranking must be truncated is typically left to the user and habitually fixed near 2,000. Relying on such a convention carries hidd...

Zhao Li, A. James, Sheng-Xuan Li · bioRxiv · 0 citations