Metadata-Version: 2.4
Name: multiqc_xenium_extra
Version: 1.0.2
Summary: MultiQC plugin for extra Xenium spatial transcriptomics analysis
Author-email: Phil Ewels <phil.ewels@seqera.io>
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.
        
Project-URL: Repository, https://github.com/MultiQC/multiqc-xenium-extra
Keywords: bioinformatics,biology,spatial transcriptomics,xenium,quality control
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: multiqc>=1.32
Requires-Dist: polars>=0.18.0
Requires-Dist: scipy>=1.8.0
Requires-Dist: scanpy>=1.9.0
Dynamic: license-file

# 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: 50000000000 # 50GB
```

## 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.
