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Achievement: Pull SharkAchievement: YOLO

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Zac-lzh/README.md

Hi, I'm Zac-lzh 👋

Bioinformatics | Single-cell | Spatial Omics | OmicVerse core contributor

ORCID Google Scholar

🔬 Research Interests

  • Single-cell transcriptomics (scRNA-seq)
  • Spatial transcriptomics & spatial omics
  • Cell-cell communication networks
  • Gene co-expression network analysis (WGCNA)
  • Tumor microenvironment & immune infiltration
  • R/Bioconductor to Python porting with numerical parity

🛠️ My Projects in OmicVerse

py-hdWGCNA
Weighted Gene Co-expression Network Analysis
Python | 3.1x faster than R | hME r=0.9999 		py-Augur
Cell Type Prioritization
Python | 4.1x faster | Pearson r=0.9999 		py-Statial
Spatial Cell State Analysis
Python | 13.6x faster | 93.8% function coverage
py-CellCall
Intercellular Network Inference
Python | 4.8x faster | Pearson >= 0.998 		py-scmetabolism
Single-cell Metabolism Analysis
Python 		py-SigXTalk
Pathway Crosstalk from Cell Communication
Python | Deep Learning
py-SpaceTrooper
QC for Image-based Spatial Transcriptomics
Python 		py-spanorm
Spatially-aware Normalisation
Python | Spatial Transcriptomics 		py-spotsweeper
Spatially-aware QC Outlier Detection
Python | Spatial Transcriptomics

📄 Publications

  • CDH2 as a Hub Gene Associated with Cisplatin Resistance and Prognosis in Ovarian Cancer - Int J Mol Sci (IF 5.6) | Code
  • DOCK5 in High-Grade Serous Ovarian Carcinoma - Single-cell analysis of immune infiltration | Code

📊 GitHub Stats

GitHub Stats

Top Languages

🔧 Tech Stack

Python R Rust Scanpy AnnData CellChat PyTorch GitHub Actions

"Porting the R bioinformatics ecosystem to Python, one package at a time."

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  1. omicverse/py-scmetabolism omicverse/py-scmetabolism Public

    Python reimplementation of scMetabolism for single-cell metabolism analysis.

    Python 2 2

  2. omicverse/py-hdWGCNA omicverse/py-hdWGCNA Public

    A pure-Python re-implementation of hdWGCNA for weighted gene co-expression network analysis in single-cell RNA-seq data.

    Python 3 3