MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. - Krishna R. Kalari; Asha A. Nair; Jaysheel D. Bhavsar; Daniel R. O'Brien; Jaime I. Dávila; Matthew A. Bockol; Jinfu J. Nie; Xiaojia Tang; Saurabh Baheti; Jay B. Doughty; Sumit Middha; Hugues Sicotte; et al. (BMC Bioinform., 2014)

PVAAS: identify variants associated with aberrant splicing from RNA-seq. - Liguo Wang 002; Jinfu J. Nie; Jean-Pierre A. Kocher (Bioinform., 2015)

Measure transcript integrity using RNA-seq data. - Liguo Wang 002; Jinfu J. Nie; Hugues Sicotte; Ying Li; Jeanette E. Eckel-Passow; Surendra Dasari; Peter T. Vedell; Poulami Barman; Liewei Wang; Richard Weinshiboum; Jin Jen; Haojie Huang; et al. (BMC Bioinform., 2016)

CpGtools: a python package for DNA methylation analysis. - Ting Wei; Jinfu J. Nie; Nicholas B. Larson; Zhenqing Ye; Jeanette E. Eckel-Passow; Keith D. Robertson; Jean-Pierre A. Kocher; Liguo Wang 002 (Bioinform., 2021)