SpatialMST
Spatial Multimodal Self-supervised Transformer
- Free software: MIT License
Installation
Create environment
conda create -n SpatialMSTEnv python=3.11
conda activate SpatialMSTEnv
Install ipykernel
conda install ipykernel
python -m ipykernel install --user --name SpatialMSTEnv --display-name "Python(SpatialMSTEnv)"
Install POT: Python Optimal Transport
conda install -c conda-forge pot
Install Pytorch and pytorch-geometric
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu129
pip install torch_geometric
Install SpatialMST
PyPI package: https://pypi.org/project/SpatialMST
pip install SpatialMST
The source files for SpatialMST can be downloaded from the Github repo.
You can either clone the public repository:
git clone https://github.com/Angione-Lab/SpatialMST.git
Once you have a copy of the source, you can install it with:
cd spatialmst
uv pip install .
Generate metabolic module flux rates and metabolite abundances for spatial transcriptomics using scFEA.
The estimated metabolic module flux rates and metabolite abundances construct the two modalities and the spatial transcriptomics data represents the third modality.
https://www.biorxiv.org/content/10.1101/2020.09.23.310656v1.full Github link
Integrating spatial transcriptomics with metabolic module fluxes and metabolite abundance:
Tutorial on multimodal integration and analysis
Download the datasets from figshare
3 maintainers
Metadata
3 maintainers
Release files for SpatialMST 0.0.4
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
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| spatialmst-0.0.4.tar.gz | 11.3 kB | Without provenance | Details for spatialmst-0.0.4.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| spatialmst-0.0.4-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details for spatialmst-0.0.4-py2.py3-none-any.whl |
Total release size: 25.6 kB
Release files / spatialmst-0.0.4.tar.gz
| Download URL | spatialmst-0.0.4.tar.gz |
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| Size | 11.3 kB |
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Release files / spatialmst-0.0.4-py2.py3-none-any.whl
| Download URL | spatialmst-0.0.4-py2.py3-none-any.whl |
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| Size | 14.3 kB |
| Tags | Python 2 Python 3 |
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