ComBatFamQC

ComBatFamQC is an R package that integrates batch effect diagnostics, data harmonization, and post-harmonization analysis for multi-site studies.

It combines interactive visualization and statistical testing to help users detect unwanted site effects, harmonize data across scanners or batches, and analyze results in a single, integrated workflow.

Key Features

ComBatFamQC integrates several powerful tools that guide users through the complete harmonization process, from detecting batch effects to generating harmonized and analysis-ready data.

Built-in Harmonization

• Provides four harmonization methods:
  ComBat, Longitudinal ComBat, ComBat-GAM, and CovBat
  
• Preserves important covariates such as age, sex, and diagnosis
  
• Produces harmonized data that are directly comparable across sites

Batch Effect Diagnostics

• Identify and measure batch effects through interactive visualizations and statistical tests
  
• Evaluate harmonization quality and detect remaining site-related variation

Post-Harmonization Analysis

• Visualize life-span age trends across brain regions
  
• Generate covariate-corrected residuals for downstream statistical or machine learning analyses

Usage Options

ComBatFamQC offers two user-friendly ways to fit different analysis needs:

• R Shiny interface for interactive exploration and visualization
  
• Command-line tools for automated and large-scale processing:
  CombatQC_CLI.R for diagnostics and harmonization
  post_CLI.R for post-harmonization visualization and residual generation

Learn More

• Visit Get Started for installation, command-line usage, and vignette access.