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SpatialHackathon / SpaceHack2023

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Native stardust #286

Closed Jieran-S closed 3 months ago

Jieran-S commented 4 months ago

So added stardust implementation of different configs...

I also changed the script a bit. I do this to avoid repeated computation when screening for resolution parameters.

In our previous script, the resolution screening requires running the autostardust or weightedstardust function over and over again. This function is basically a wrapper for an entire Seurat pipeline. So running them again results in a repeated calculations of scTranscform and createSeuratobjects etc. I broke the wrapper down and now the resolution screening only requires screening of the last step.

Jieran-S commented 4 months ago

Update:

  1. Add n_pcs into input params
  2. Add binary_search function by calling the script
  3. Remove redundant configs

As the stardust pipeline doesn't have an HVG function, I didn't add one hence.