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SpatialHackathon / SpaceHack2023

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Cluster parameter, neighbors defintion & other issues for method implementation #198

Open Jieran-S opened 6 months ago

Jieran-S commented 6 months ago

Some issues I found in the current implementation:

  1. Some implementation omits customized preprocess steps: DeepST. did @shdam find anything from the methods you worked on?

  2. Some implementations don't use existing neighbor graphs: scanpy, seurat, SOTIP all use standard scanpy or seurat neighbor construction methods. They can use existing neighbor graphs

  3. Clustering using resolution instead of clusters_number: SOTIP, SpaceFlow, STAGATE, SCAN-IT. Can implement grid-search to convert resolution into cluster_number definition.

Would these issues make sense? if so I will update them @niklasmueboe @naveedishaque

shdam commented 6 months ago

Regarding 3. Seurat and stardust have the same issue. I implemented a resolution tuning function for those.