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bio-workflows-spatial-pipeline

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End-to-end spatial transcriptomics analysis workflow.

Data & Analytics#domain-detection#spatial-transcriptomics#scanpy#xenium#spatial-analysis#visium#squidpy
Authorya-way
Version1.0.0
Installs0

System Documentation

What problem does it solve?

End-to-end spatial transcriptomics analysis is complex and time-consuming; this workflow automates data loading, QC, normalization, clustering, spatial analysis, domain detection, and visualization to deliver interpretable tissue maps.

Core Features & Use Cases

  • Load spatial data from Visium/Xenium outputs
  • Perform QC, normalization, HVG selection, clustering, and spatial analysis
  • Detect tissue domains and visualize spatial gene expression patterns
  • Use case: researchers can rapidly obtain spatial domains and marker genes for tissue sections

Quick Start

Run the spatial pipeline on your Visium spaceranger_output or Xenium results to begin analysis.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: bio-workflows-spatial-pipeline
Download link: https://github.com/ya-way/cytoclaw-skills/archive/main.zip#bio-workflows-spatial-pipeline

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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