GeneSwitches: ordering gene expression and functional events in single-cell experiments. - Elaine Y. Cao; John F. Ouyang; Owen J. L. Rackham (Bioinform., 2020)

ShinyCell: simple and sharable visualization of single-cell gene expression data. - John F. Ouyang; Uma S. Kamaraj; Elaine Y. Cao; Owen J. L. Rackham (Bioinform., 2021)

scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets. - Yi Xie; Jianfei Yang; John F. Ouyang; Enrico Petretto (Briefings Bioinform., 2024)