| Name | multiqc-xenium-extra JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | MultiQC plugin for extra Xenium spatial transcriptomics analysis |
| upload_time | 2025-10-25 22:17:27 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License
Copyright (c) 2024 Phil Ewels
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
bioinformatics
biology
spatial transcriptomics
xenium
quality control
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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
```bash
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:
```yaml
log_filesize_limit: 5000000000 # 5GB
```
## Usage
Once installed, the plugin automatically extends the Xenium module when you run MultiQC:
```bash
multiqc /path/to/xenium/data
```
The extra sections will appear alongside the core Xenium module sections in the report.
Raw data
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