SpaMV: An interpretable spatial multi-omics data integration and dimension reduction algorithm
Installation
- Create and activate a conda environment with python 3.12
conda env create spamv python==3.12
conda activate spamv
- (Optional) If you want to apply our algorithm to large datasets (with more than 10,000 spots), please make sure you have installed the pyg-lib package.
pip install pyg-lib -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
where
${TORCH}should be replaced by either1.13.0,2.0.0,2.1.0,2.2.0,2.3.0,2.4.0,2.5.0,2.6.0, or2.7.0${CUDA}should be replaced by eithercpu,cu102,cu117,cu118,cu121,cu124,cu126, orcu128
- Then you can install our package as follows:
pip install spamv
Tutorial
We provide two jupyter notebooks (Tutorial_simulation.ipynb and Tutorial_realworld.ipynb) to reproduce the results in our paper. Before you run them, please make sure that you have downloaded the simulated data and/or real-world data from our Zenodo repositoy.
1 maintainer
Release files for SpaMV 1.0.45
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| spamv-1.0.45.tar.gz | 30.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| spamv-1.0.45-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 62.6 kB
Release files / spamv-1.0.45.tar.gz
| Download URL | spamv-1.0.45.tar.gz |
|---|---|
| Size | 30.7 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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No |
| Uploaded via |
twine/6.2.0 CPython/3.14.2
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Release files / spamv-1.0.45-py3-none-any.whl
| Download URL | spamv-1.0.45-py3-none-any.whl |
|---|---|
| Size | 31.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.14.2
|
