MOVICS: an R package for multi-omics integration and visualization in cancer subtyping. - Xiaofan Lu; Jialin Meng; Yujie Zhou; Liyun Jiang; Fangrong Yan (Bioinform., 2021)

PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data. - Xinjia Ruan; Yu Cheng; Yuqing Ye; Yuhang Wang; Xinyi Chen; Yuqing Yang; Tiantian Liu; Fangrong Yan (Briefings Bioinform., 2024)

Accounting for the impact of rare variants on causal inference with RARE: a novel multivariable Mendelian randomization method. - Yu Cheng; Xinjia Ruan; Xiaofan Lu; Yuqing Yang; Yuhang Wang; Shangjin Yan; Yuzhe Sun; Fangrong Yan; Liyun Jiang; Tiantian Liu (Briefings Bioinform., 2025)