Projects

SCMER (2021)

Manifold based feature selection.

• Use cases: single-cell assays (scRNA-seq, scATAC-seq, CITE-seq, CyTOF, …)
• Publication: “Single-cell manifold-preserving feature selection for detecting rare cell populations.” Nature Computational Science 1.5 (2021): 374-384.
• Python package (and R wrapper): https://github.com/KChen-lab/scmer
• Tutorials: https://scmer.readthedocs.io/en/latest/examples.html

EpiNB (2022)

A package for MHC-I antigen presentation prediction.

• web app: https://epinbweb.streamlit.app/
• Python package: https://github.com/KChen-lab/epiNB

Sensei (2021)

• Publication: “Sensei: how many samples to tell a change in cell type abundance?.” BMC bioinformatics 23 (2022): 1-22.
• web app: https://kchen-lab.github.io/sensei/table_beta.html

Weighted common-language effect size for the van Elteren Test (2020)

• Publication: “Stratified Test Accurately Identifies Differentially Expressed Genes Under Batch Effects in Single-Cell Data.” IEEE/ACM transactions on computational biology and bioinformatics 18.6 (2021): 2072-2079.
• R code: https://github.com/KChen-lab/stratified-tests-for-seurat

Cyclum (2019)

• Publication: “Latent periodic process inference from single-cell RNA-seq data.” Nature communications 11.1 (2020): 1441.
• Python package: https://github.com/KChen-lab/cyclum