sc-batch-integration

What problem does it solve?

This Skill addresses the challenge of technical variation (batch effects) in single-cell RNA sequencing data, which can obscure true biological differences between samples.

Core Features & Use Cases

• Batch Effect Removal: Integrates multiple scRNA-seq datasets to remove technical variation while preserving biological signals.
• Method Flexibility: Supports various state-of-the-art integration algorithms including Harmony, scVI, Seurat CCA/RPCA, BBKNN, and fastMNN.
• Use Case: Integrate data from experiments run on different days or with different reagent lots to enable a unified downstream analysis, such as identifying cell types or differential gene expression across all conditions.

Quick Start

Run Harmony batch integration on my merged single-cell data.