integration-harmony
CommunityBatch-correct spatial slices with Harmony.
Data & Analytics#integration#harmony#spatial-transcriptomics#batch-correction#pca#multi-slice#knn-transfer
Authorchenyhvvvv
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Batch integration of multiple spatial transcriptomics slices to remove batch effects and enable joint analysis, preserving cell-type interpretation across slices.
Core Features & Use Cases
- Harmony batch correction in PCA space to align slices
- Optional: incorporate a reference scRNA-seq with celltype annotations for KNN label transfer
- Store integrated embeddings back into each slice for downstream analysis and provenance
- Compare pre- and post-integration UMAPs to assess batch correction quality
Quick Start
Run Harmony integration by specifying the slices to merge and an optional reference path, then inspect the harmonized embeddings in each slice.
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: integration-harmony Download link: https://github.com/chenyhvvvv/STAT-agent/archive/main.zip#integration-harmony Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
Agent Skills Search Helper
Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.