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  • Guangzhou, China
  • 23:13 (UTC +08:00)

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l-zh007/README.md

Jack GitHub profile header

GitHub profile Spatialsnake on PyPI Spatialsnake Bioconda version Spatialsnake documentation Profile views

Research and development interests

About Me

  • Jack · Bioinformatics undergraduate based in Guangzhou, China
  • Interested in computational methods for spatial transcriptomics, single-cell omics, and multi-omics integration
  • Developing reproducible workflows and open-source software for biological data analysis

Research Interests

Computational methods for reproducible, scalable, and biologically interpretable omics analysis

Spatial transcriptomics Single-cell omics

Multi-omics integration Deep learning for genomics

Featured Project

Spatialsnake

Spatialsnake is an open-source, user-friendly Linux command-line application for reproducible spatial transcriptomics analysis. It uses SpatialData and Snakemake to organize platform-specific inputs into modular analyses covering data ingestion, quality control, preprocessing, clustering, annotation support, and downstream biological exploration.

Spatialsnake source code Spatialsnake documentation Spatialsnake package Spatialsnake supported platforms Spatialsnake Bioconda downloads

Technical Stack

Programming Languages

Java, Python, and R

Workflow and Development

Linux, Git, GitHub, Docker, and Visual Studio Code

Snakemake workflow management Bioconda package distribution

Bioinformatics Ecosystem

SpatialData Scanpy Squidpy Seurat scverse

Contribution Activity

GitHub contribution activity

Bioinformatics · Spatial Omics · Reproducible Research · Open-Source Software

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