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.
Release files for multiqc-xenium-extra 1.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| multiqc_xenium_extra-1.0.2.tar.gz | 24.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| multiqc_xenium_extra-1.0.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 47.6 kB
Release files / multiqc_xenium_extra-1.0.2.tar.gz
| Download URL | multiqc_xenium_extra-1.0.2.tar.gz |
|---|---|
| Size | 24.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.7
|
Release files / multiqc_xenium_extra-1.0.2-py3-none-any.whl
| Download URL | multiqc_xenium_extra-1.0.2-py3-none-any.whl |
|---|---|
| Size | 23.6 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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|
BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.7
|
