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Add example dataset loading #5

Merged
merged 4 commits into from
Jul 3, 2024
Merged

Add example dataset loading #5

merged 4 commits into from
Jul 3, 2024

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casblaauw
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@casblaauw casblaauw commented Jun 27, 2024

Adds crested.get_dataset(), currently with support for BICCN topic bed and peak bigwig datasets. Example dataset names (currently "mouse_cortex_bed"/"mouse_cortex_bigwig") can still be changed, but do remember to change introduction.ipynb as well.

Open questions/to-do:

  • Add melanoma and fly brain data
  • Add DARs for transfer learning example (on whichever dataset we end up showing that)
  • Should we refer to a tutorial to preprocess data like this?
    • If so, should it be to get these specific files (esp for topics: BICCN with this topic modeling and otsu cutoffs), or is referring to pycisTopic/snapATAC2 tutorials enough?

@LukasMahieu LukasMahieu merged commit c0e0de6 into main Jul 3, 2024
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@LukasMahieu
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I'm already merging this since there are no conflicts anyway and I want to test with new main branch functionality.
Feel free to continue working on this in this branch and create a new PR later.

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