pathway-ssgsea
CommunityPer-cell pathway activity scoring with ssGSEA.
Data & Analytics#spatial-transcriptomics#anndata#pathway#gene-sets#msigdb#ssgsea#single-sample-enrichment
Authorchenyhvvvv
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Scores per-cell pathway activity in spatial transcriptomics data using ssGSEA to reveal spatial variation in pathway activation.
Core Features & Use Cases
- Supports per-cell ssGSEA scoring across tissues to visualize pathway activation
- Compatible with MSigDB Hallmark, KEGG, GO, and custom gene sets
- Outputs: per-cell pathway scores stored in adata.obs (ssgsea_<pathway>) and parameters in adata.uns
Quick Start
Apply ssGSEA to your single-slice spatial data to compute per-cell pathway scores and visualize them on the spatial canvas.
Dependency Matrix
Required Modules
None requiredComponents
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: pathway-ssgsea Download link: https://github.com/chenyhvvvv/STAT-agent/archive/main.zip#pathway-ssgsea Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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