It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR. - Aaron T. L. Lun; Yunshun Chen; Gordon K. Smyth (Statistical Genomics, 2016)

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. - Yunshun Chen; Aaron T. L. Lun; Gordon K. Smyth (F1000Research, 2016)

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR. - Yunshun Chen; Bhupinder Pal; Jane E. Visvader; Gordon K. Smyth (F1000Research, 2017)

Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data. - Jinming Cheng; Xinyi Jin; Gordon K. Smyth; Yunshun Chen (BMC Bioinform., 2025)

Incorporating exon-exon junction reads enhances differential splicing detection. - Mai T. Pham; Michael J. G. Milevskiy; Jane E. Visvader; Yunshun Chen (BMC Bioinform., 2025)