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
pip install multiqc-xenium-extra- MultiQC >= 1.20
- polars >= 0.18.0
- scipy >= 1.8.0
- scanpy >= 1.9.0
The plugin automatically adjusts the file size limit to handle large Xenium files:
log_filesize_limit: 50000000000 # 50GBOnce installed, the plugin automatically extends the Xenium module when you run MultiQC:
multiqc /path/to/xenium/dataThe extra sections will appear alongside the core Xenium module sections in the report.