Seurat — Integration & Batch Correction

Real experiments have multiple samples from different batches. Learn to integrate them with Harmony and Seurat CCA — and understand when to use each. Remove batch effects without removing real biological signal.

Week 34Timeline

~7 hrsStudy time

FREEAlways

Start Lesson 1 → View in curriculum →

What you'll learn

Topics covered in this module

Harmony integration

Seurat CCA

DoubletFinder

Multi-sample UMAP

Before/after comparison

Integration anchors

Label transfer · Azimuth

LISI mixing scores

Curriculum

10 lessons in this module

1Why Batch Effects Exist & How Integration WorksLive

2Setting Up Multi-Sample Seurat ObjectsSoon

3Anchor-Based Integration with FindIntegrationAnchorsSoon

4IntegrateData & Running the Integrated WorkflowSoon

5Harmony Integration — Fast & ScalableSoon

6Evaluating Integration Quality (LISI, mixing scores, UMAPs)Soon

7Label Transfer Across DatasetsSoon

8Reference-Based Mapping with AzimuthSoon

9Integrating Plant scRNA-seq Datasets (Sorghum context)Soon

10Capstone: Full Multi-Batch Integration PipelineSoon

📋 Not sure where this fits? Module 26 is part of the full bioinformatics curriculum — a structured 42-week learning path from Bash to single-cell RNA-seq.

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Lesson 1 is live. The rest are on their way.

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Module 26 of 31