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Add SpaGFT-like method for identification of SVGs #901

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timtreis opened this issue Oct 15, 2024 · 0 comments
Open

Add SpaGFT-like method for identification of SVGs #901

timtreis opened this issue Oct 15, 2024 · 0 comments
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enhancement ✨ New feature or request graph 🕸️ squidpy2.0 Everything releated to a Squidpy 2.0 release

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@timtreis
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SpaGFT (Spatial omics representation and functional tissue module inference using graph Fourier transform) uses Fourier transforms to identify SVGs (and then groups them into "tissue modules". At SBI2 the presenter said their method is "similar but better than Moran's I" - so we could potentially implement it as another flavor in https://squidpy.readthedocs.io/en/stable/api/squidpy.gr.spatial_autocorr.html.

The implementation already used AnnData and looks to be low on dependencies:
https://github.com/jxLiu-bio/SpaGFT/blob/master/SpaGFT/gft.py

@timtreis timtreis added enhancement ✨ New feature or request graph 🕸️ squidpy2.0 Everything releated to a Squidpy 2.0 release labels Oct 15, 2024
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Labels
enhancement ✨ New feature or request graph 🕸️ squidpy2.0 Everything releated to a Squidpy 2.0 release
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