harmony-batch-correction

Name: harmony-batch-correction
Availability: InStock
Author: jaechang-hits

Remove technical batch effects from PCA embeddings in single-cell omics data.

298|27|Updated Feb 18, 2026

Search Tags:#harmony #single-cell #batch correction #data integration #omics #scRNA-seq

Ready to run

npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill harmony-batch-correction

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: harmony-batch-correction
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/harmony-batch-correction
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill harmony-batch-correction

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires harmonypy, scanpy, leidenalg, igraph, anndata, pandas, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill addresses the challenge of removing technical batch effects from single-cell omics data, ensuring that biological variation is preserved while integrating datasets from different sources.

Core Features & Use Cases

Batch Effect Removal: Integrates datasets by regressing out technical variations from PCA embeddings.
Scalability: Efficiently handles datasets with millions of cells.
Use Case: Combine scRNA-seq data from multiple experiments or labs to identify cell types consistently across all batches.

Quick Start

Use the harmony-batch-correction skill to integrate the provided AnnData object using the 'batch' column.

Frequently Asked Questions about harmony-batch-correction

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I perform batch correction on scRNA-seq data from multiple experiments?▼

Batch correction on scRNA-seq data integrates datasets from multiple experiments by removing technical batch effects from PCA embeddings using the Harmony algorithm while preserving biological variation.

Can I use harmonypy with scanpy to integrate millions of cells?▼

Yes, harmonypy works with scanpy to perform scalable batch correction, efficiently integrating datasets containing millions of cells by regressing out technical variations from PCA embeddings.

What is the best way to integrate single-cell omics data while preserving biological variation?▼

Integrating single-cell omics data while preserving biological variation is achieved through Harmony batch correction, which regresses out technical batch effects from PCA embeddings to identify cell types consistently.

Does Harmony batch correction work with both Python and R workflows?▼

Harmony batch correction supports both Python workflows using harmonypy and scanpy, and R workflows using Seurat, providing scalable integration for single-cell omics data across disparate sources.

How do I integrate an AnnData object using a specific batch column for single-cell data integration?▼

To integrate an AnnData object, use the harmony-batch-correction skill and specify the 'batch' column, which allows the algorithm to identify and regress out technical variations from the PCA embeddings.