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env
env
 
 
.gitignore
.gitignore
 
 
1_LIBD_DLPFC.ipynb
1_LIBD_DLPFC.ipynb
 
 
1_SDMbench_download.ipynb
1_SDMbench_download.ipynb
 
 
2_Banksy.ipynb
2_Banksy.ipynb
 
 
2_BayesSpace_DLPFC.ipynb
2_BayesSpace_DLPFC.ipynb
 
 
2_Leiden_DLPFC.ipynb
2_Leiden_DLPFC.ipynb
 
 
2_Leiden_SDMbench_dataset.ipynb
2_Leiden_SDMbench_dataset.ipynb
 
 
2_SpaGCN_DLPFC.ipynb
2_SpaGCN_DLPFC.ipynb
 
 
2_SpatialEmbedding_effect.ipynb
2_SpatialEmbedding_effect.ipynb
 
 
2_SpiceMix.ipynb
2_SpiceMix.ipynb
 
 
2_X_with_SpatialLeiden.ipynb
2_X_with_SpatialLeiden.ipynb
 
 
3_Fig.ipynb
3_Fig.ipynb
 
 
3_Fig_schematic.ipynb
3_Fig_schematic.ipynb
 
 
3_SuppFigs.ipynb
3_SuppFigs.ipynb
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
benchmark.py
benchmark.py
 
 
downloads.tsv
downloads.tsv
 
 
spicemix.py
spicemix.py
 
 
utils.py
utils.py
 
 

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SpatialLeiden - Study

Code to reproduce results for the study

Müller-Bötticher, N., Sahay, S., Eils, R., and Ishaque, N. "SpatialLeiden - Spatially-aware Leiden clustering" bioRxiv (2024) https://doi.org/10.1101/2024.08.23.609349

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doi.org/10.1186/s13059-025-03489-7

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