scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. - Luyi Tian; Shian Su; Xueyi Dong; Daniela Amann-Zalcenstein; Christine Biben; Azadeh Seidi; Douglas J. Hilton; Shalin H. Naik; Matthew E. Ritchie (PLoS Comput. Biol., 2018)

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods. - Shian Su; Luyi Tian; Xueyi Dong; Peter F. Hickey; Saskia Freytag; Matthew E. Ritchie (Bioinform., 2020)

Benchmarking long-read RNA-seq analysis methods. - Xueyi Dong (2022)