MultiQC Xenium Extra Plugin

Advanced analysis plugin for Xenium spatial transcriptomics data in MultiQC.

This plugin extends the core MultiQC Xenium module with computationally intensive analyses including:

• Parquet file processing (transcripts.parquet, cells.parquet)
• H5 matrix analysis (cell_feature_matrix.h5)
• Distribution plots (density, violin, box plots)
• Cell area and nucleus analysis
• Transcript quality distributions
• FoV quality heatmaps

Installation

pip install multiqc-xenium-extra

Requirements

• MultiQC >= 1.20
• polars >= 0.18.0
• scipy >= 1.8.0
• scanpy >= 1.9.0

Configuration

The plugin automatically adjusts the file size limit to handle large Xenium files:

log_filesize_limit: 5000000000 # 5GB

Usage

Once installed, the plugin automatically extends the Xenium module when you run MultiQC:

multiqc /path/to/xenium/data

The extra sections will appear alongside the core Xenium module sections in the report.