I am a tenure-track Assistant Professor in Department of Biostatistics and Bioinformatics at Duke University.
My primary research interest is developing novel statistical and computational methods for integrating and analyzing big and complex genomic data, especially data from single-cell sequencing and spatial transcriptomics. Some examples include the differential analysis of single-cell RNA-sequencing (scRNA-seq) data with multiple samples, joint analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data, pseudotime trajectory inference, and signal recovery for single-cell ATAC-sequencing (scATAC-seq) data. I have been actively applying these methods to various biological and clinical studies, such as immunology and cancer.
Name | Type | Author | Availability |
---|---|---|---|
SCATE: Single-cell ATAC-seq signal extraction and enhancement | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] |
TSCAN: Tools for Single-Cell ANalysis | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] [Bioconductor] [Online GUI] |
BIRD: Big data regression for predicting DNase I hypersensitivity | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] |
SCRAT: Single-Cell Regulome Analysis Tool | R Software Package | Zhicheng Ji, Weiqiang Zhou, Hongkai Ji | [Github] [Online GUI] |
STIP: State transition inference prediction | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] |
GSCA: Gene Set Context Analysis | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] [Bioconductor] [Online GUI] |
RMRCE: Regularized Maximum Rank Correlation Estimator | R Software Package | Fang Han, Hongkai Ji, Zhicheng Ji, Honglang Wang | [Github] |
SEPA: Single-cell Gene Expression Pattern Analysis | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] [Bioconductor] [Online GUI] |
GEOsearch: Extendable Search Engine for GEO | R Software Package | Zhicheng Ji, Hongkai Ji | [Github] [Bioconductor] [Online GUI] |
Reproducible Interactive Data Exploration Tool | Web Application | Zhicheng Ji, Hongkai Ji | [Online GUI] |
Email:
zhicheng.ji@duke.edu
Github:
https://github.com/zji90