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Implement from_Seurat and to_Seurat #60

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rcannood opened this issue May 3, 2023 · 4 comments · Fixed by #64
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Implement from_Seurat and to_Seurat #60

rcannood opened this issue May 3, 2023 · 4 comments · Fixed by #64
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@rcannood @csangara @bschilder
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enhancement New feature or request
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1.0.0

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@rcannood
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rcannood commented May 3, 2023

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@rcannood rcannood self-assigned this May 3, 2023
@rcannood rcannood added this to the 0.1.0 milestone May 3, 2023
This was referenced May 4, 2023
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@LouiseDck LouiseDck reopened this Sep 15, 2023
@LouiseDck LouiseDck moved this to 📋 Backlog in Ghent Hackathon 2023 Sep 15, 2023
@bschilder bschilder added the enhancement New feature or request label Sep 18, 2023
@berombau berombau moved this from 📋 Backlog to 🏗 In progress in Ghent Hackathon 2023 Sep 18, 2023
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bschilder commented Sep 18, 2023 •
edited by csangara
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from_Seurat strategy

  • Only support single-assays when converting to "AbstractAnnData".
  • When a Seurat object has >1 assay, tell the user the Default assay is being used.
  • Also allow the user to select which assay they want to use.
  • Alternatively, could store original assay name in uns slot. If the stored assay name is available, use that, if not use the default "RNA".
  • Turn each matrix element within the selected assay into layers (counts, data, scaled.data).
  • Set X as counts matrix element by default, as you can always normalise/manipulate the data from afterwards. However, allow the user the option of setting X=NULL
  • Enable conversion of obsm slot
  • Enable conversion of varm slot

to_Seurat strategy

  • Check names of layers, and if they correspond to canonical Seurat matrix element names (counts, data, scaled.data), assign them accordingly.
  • Allow the user to set the assay name. If NULL, will set to Seurat default assay name ("RNA").
  • When X is not provided, use first layer as assay data, and the rest as additional assays.
  • When neither X nor layers are provided, throw error.
  • Enable conversion of obsm slot
  • Enable conversion of varm slot

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@rcannood rcannood changed the title Implement from_Seurat Implement from_Seurat and to_Seurat Sep 18, 2023
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Sounds good, thanks!

@csangara csangara mentioned this issue Sep 19, 2023
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@bschilder @rcannood By the way, I will not have time to work on this anymore before the deadline. You can see what I've done so far in the issue-60-from-seurat-obsm-varm branch. I didn't get to test it very much yet so some parts will probably not work.

@LouiseDck LouiseDck mentioned this issue Sep 27, 2023
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rcannood commented Nov 5, 2024

Fixed by #183

@github-project-automation github-project-automation bot moved this from 🏗 In progress to ✅ Done in Ghent Hackathon 2023 Dec 12, 2024
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enhancement New feature or request
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initial implementation of from_Seurat scverse/anndataR
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@rcannood @csangara @bschilder @LouiseDck