Software
We develop computational tools for single-cell, spatial, and multi-omics data analysis. This page collects lab software, packages, analysis code, and related publications.
Φ-Space
Continuous phenotyping of single-cell multi-omics data.
- Related paper: Mao, J., Deng, Y. & Lê Cao, K.-A. (2024). Φ-Space: Continuous phenotyping of single-cell multi-omics data. Genome Biology.
- Software link: Placeholder.
Φ-Space ST
A platform-agnostic method to identify cell states in spatial transcriptomics studies.
- Related paper: Mao, J., Choi, J. & Lê Cao, K.-A. (2026). Φ-Space ST. Cell Reports Methods.
- Seminar recording: https://mixomics.org/2025/02/webinar-%cf%86-space-st-a-platform-agnostic-method-to-identify-cell-states-in-spatial-transcriptomics-studies/
- Software link: Placeholder.
NeighbourNet
Scalable cell-specific coexpression networks for granular regulatory pattern discovery.
- Related paper: Deng, Y., Mao, J., Choi, J. & Lê Cao, K.-A. (2026). Genome Research.
- Software link: Placeholder.
phylobar
An R package for multiresolution compositional barplots in omics studies.
- Related paper: Kuo, M., Lê Cao, K.-A., Kodikara, S., Mao, J., Sankaran, K. (2025). Bioinformatics.
- Software link: Placeholder.
CellDiffusion
A generative model to annotate single-cell and spatial RNA-seq using bulk references.
- Related paper: Zhang, X., Mao, J. & Lê Cao, K.-A. (2025). bioRxiv.
- Software link: Placeholder.
Other Analysis Code
Placeholder: add links for StableMate, DIVAS, workshop repositories, analysis code for publications, and lab GitHub repositories.