Background
A pthon package build on top of spatialdata for Single-Cell In-Situ Spatial-Omics data analysis, developped to handle Vizgen (merscope), Nanostring (cosmx) and 10xGenomics (Xenium) experiments.
Features
- Read in-situ spatial-omics assays experiments: build on top of spatialdata package
- Automatic cell type annotation: scanvi implementation
- Import anatomical .csv shape file from xenium explorer: as anndata observations
- Automatic run pseudobulk data analysis: using decoupler and pydeseq2 packages
- Compute cell type proportion in region: integrating statistical test in case of replicates
- Produce high quality spatial figures: build on top of spatialdata_plot package
Getting started
Please refer to the documentation. In particular, the
Installation
- Create a conda environment (Python >= 3.11)
- Install sparty using pip:
conda create -n sparty python==3.11
conda activate sparty
pip install git+https://github.com/cobioda/sparty.git@main
Contribution
If you found a bug or you want to propose a new feature, please use the issue tracker.
1 maintainer
Metadata
1 maintainer
Release files for sparty 0.1.0
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| sparty-0.1.0.tar.gz | 92.8 kB | Without provenance | Details for sparty-0.1.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| sparty-0.1.0-py3-none-any.whl | Python 3 | none | any | Details for sparty-0.1.0-py3-none-any.whl |
Total release size: 170.9 kB
Release files / sparty-0.1.0.tar.gz
| Download URL | sparty-0.1.0.tar.gz |
|---|---|
| Size | 92.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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twine/6.2.0 CPython/3.13.0
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Release files / sparty-0.1.0-py3-none-any.whl
| Download URL | sparty-0.1.0-py3-none-any.whl |
|---|---|
| Size | 78.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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twine/6.2.0 CPython/3.13.0
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