MultiQC plugin for extra Xenium spatial transcriptomics analysis
Project description
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: 50000000000 # 50GB
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.
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