Software

I develop R packages for single-cell and spatial omics analysis.

Bioconductor Packages

RankMap

An R/Bioconductor package for rank-based reference mapping of spatial and single-cell transcriptomics data.

• Bioconductor: https://bioconductor.org/packages/RankMap/
• GitHub: https://github.com/jinming-cheng/RankMap/
• Since: 2026 on Bioconductor, 2025 on GitHub
• Citation: Cheng et al. 2026. bioRxiv.

SpNeigh

An R/Bioconductor package for boundary-aware spatial neighborhood and differential expression analysis.

• Bioconductor: https://bioconductor.org/packages/SpNeigh/
• GitHub: https://github.com/jinming-cheng/SpNeigh/
• Since: 2026 on Bioconductor, 2025 on GitHub
• Citation: Cheng et al. 2026. NAR Genomics and Bioinformatics.

Other R Packages

scTernary

An R package for ternary plot analysis of single cell RNA-seq data.

• GitHub: https://github.com/jinming-cheng/scTernary/
• Since: 2022 on GitHub