Cases Skills About

bulk-rna-seq-batch-correction-with-combat - Harmonize bulk RNA-seq data across batches with ComBat

Remove batch effects from merged bulk RNA-seq or microarray cohorts using omicverse's pyComBat wrapper

Tags

Updated: 2026-02-23

RNA-seq batch-correction data-harmonization bioinformatics omics python

Capabilities

Load expression matrices Concatenate datasets by shared genes Run ComBat batch correction Export corrected matrices

Typical Inputs

Bulk expression matrices Batch metadata Gene expression tables

Typical Outputs

Corrected expression matrices Harmonized AnnData files PCA visualization plots

What this skill does

Load expression matrices
Concatenate datasets by shared genes
Run ComBat batch correction
Export corrected matrices
Visualize before/after PCA embeddings
Save harmonized AnnData files

Inputs

Bulk expression matrices
Batch metadata
Gene expression tables
Sample information

Outputs

Corrected expression matrices
Harmonized AnnData files
PCA visualization plots
Before/after correction comparisons

Requirements

omicverse library
anndata objects
pandas for data handling
matplotlib for visualization
Gene identifiers harmonization
Log-scale intensity data

Source

Spec: SKILL.md

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