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Achievement: Pair ExtraordinaireAchievement: Starstruckx3Achievement: Pull Sharkx2Achievement: Galaxy BrainAchievement: QuickdrawAchievement: YOLO

Achievements

Achievement: Pair ExtraordinaireAchievement: Starstruckx3Achievement: Pull Sharkx2Achievement: Galaxy BrainAchievement: QuickdrawAchievement: YOLO

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cafferychen777/README.md

Chen Yang (Caffery)

I am a PhD student in Statistics at Texas A&M University developing reliable machine-learning and agentic systems for scientific discovery, with current applications in spatial genomics and single-cell analysis. I work with Prof. Xianyang Zhang at Texas A&M and Prof. Jun Chen at Mayo Clinic.

Website · Google Scholar · ORCID · LinkedIn

Research

  • Reliable machine learning and agentic systems for scientific discovery
  • Spatial genomics and single-cell analysis
  • Statistical methodology and reproducible research software

Selected research software

Project Description
mLLMCelltype Multi-LLM consensus framework for automated cell type annotation in scRNA-seq
ChatSpatial Schema-enforced, MCP-based agentic platform for spatial transcriptomics
FlashDeconv Atlas-scale spatial deconvolution via structure-preserving sketching
FlashS Frequency-domain detection of spatially variable genes at atlas scale
EdgeMap Edge-centric heritability mapping through spatial cell-cell communication
ggpicrust2 R package for PICRUSt2 functional-profile analysis and visualization
MicrobiomeStat R package for longitudinal microbiome and multi-omics analysis
Overleaf CLI Command-line workflows for managing Overleaf projects

Selected publications

Selected oral presentations

  • 33rd International Biometric Conference, Seoul, 2026
  • MLGenX Workshop at ICLR, Rio de Janeiro, 2026
  • ENAR Spring Meeting, Indianapolis, 2026
  • StatCafe, Department of Statistics, Texas A&M University, 2026

For a complete list of publications, software, and presentations, visit cafferyang.com.

Pinned Loading

  1. ggpicrust2 ggpicrust2 Public

    Make Picrust2 Output Analysis and Visualization Easier

    R 205 26

  2. mLLMCelltype mLLMCelltype Public

    Cell type annotation for single-cell RNA-seq using multi-LLM consensus

    Python 661 57

  3. ChatSpatial ChatSpatial Public

    MCP server for spatial transcriptomics analysis through natural language interfaces.

    Python 44 13

  4. flashdeconv flashdeconv Public

    Fast spatial deconvolution via leverage-score sketching — scales to million-spot datasets while preserving rare cell type signals.

    Python 26

  5. EdgeMap EdgeMap Public

    Python package for partitioning GWAS heritability into cell-intrinsic (node) and cell-cell communication (edge) components from spatial transcriptomics.

    Python 3

  6. FlashS FlashS Public

    Spatially variable gene detection via frequency-domain kernel testing

    Python 1