bulk-rna-seq-batch-correction-with-combat - Bulk RNA-seq batch correction with ComBat
Remove batch effects from merged bulk RNA-seq or microarray cohorts using omicverse's pyComBat wrapper
Tags
Updated: 2026-02-23Capabilities
Typical Inputs
Typical Outputs
What this skill does
- read expression matrices
- concatenate gene expression data
- run ComBat batch correction
- export corrected matrices
- create PCA visualizations
Inputs
- pickled expression matrices
- CSV expression tables
- sample metadata
- batch information
Outputs
- corrected expression matrix
- raw expression matrix
- harmonized AnnData file
- PCA embedding plots
- before/after boxplots
Requirements
- Python environment
- omicverse library
- pandas library
- anndata library
- matplotlib library