Changhu Wang

DE-Rigor-Agent automates differential expression analysis for bulk RNA-seq by evaluating method suitability, reducing false discovery rates and improving statistical power across diverse datasets.

IntegrateRigor optimizes batch integration for cell identity recovery in single-cell and spatial transcriptomics data, revealing cancer-immune interface niches previously obscured by integration biases.

Hypatia compares isoform complexities across cell populations using long-read single-cell transcriptomes, improving detection of isoform usage shifts and diversity.

CIPHER uses gene co-fluctuations in unperturbed cells to predict transcriptome-wide responses to perturbations, outperforming existing methods and revealing key regulatory structures.

This paper introduces Festem, a method that directly selects differentially expressed genes for single-cell clustering, improving cell-type identification and reducing selection bias.