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docs: add tutorials for variants#459

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gcroci2 merged 42 commits intomainfrom
435_add_tutorials_variants_gcroci2
Sep 1, 2023
Merged

docs: add tutorials for variants#459
gcroci2 merged 42 commits intomainfrom
435_add_tutorials_variants_gcroci2

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@gcroci2 gcroci2 commented Jul 21, 2023 •
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In this PR:

  • Created a notebook for generating missense variant HDF5 files
  • Updated the training tutorial notebook and the tutorials' readme for including missense variants
  • Updated the files in docs/ and the repo's readme
  • Updated the Zenodo links after having uploaded the new data's version
  • Improved already existing tutorials and fixed broken links (Fix link in TUTORIAL.md #462)

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@gcroci2 gcroci2 self-assigned this Jul 21, 2023
@gcroci2 gcroci2 marked this pull request as draft July 21, 2023 13:51
@gcroci2 gcroci2 linked an issue Jul 21, 2023 that may be closed by this pull request
Add tutorials for variants #435
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@gcroci2 gcroci2 marked this pull request as ready for review July 25, 2023 09:41
@gcroci2 gcroci2 requested a review from DaniBodor July 26, 2023 20:50
gcroci2 and others added 2 commits July 27, 2023 10:27
@gcroci2
update zotero address
106766a
@gcroci2
Update deeprankcore/dataset.py
1821788 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
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I haven't managed to copy the raw data into my wsl environment of my new laptop, so I wasn't able to test run the notebook. Something about permissions, which I have been having difficulties with for a few different things.
So far, I have only looked at the markdown cells and glossed over the code. If you want me to test run the notebook as well, let me know and I will try to see how to move the data to wsl.

gcroci2 and others added 6 commits August 4, 2023 11:14
@gcroci2
read the defaults without hard-coding them
582e635
@gcroci2
Merge pull request #461 from DeepRank/fix_train_inheritance_warnings
50050a8 
fix: `dataset_train` inheritance warnings
@gcroci2
Update README.md
687c9a7 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update README.md
72ad74f 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update README.md
abac4f8 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/TUTORIAL.md
203b5dc 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
gcroci2 and others added 11 commits August 4, 2023 16:55
@gcroci2
Update tutorials/TUTORIAL.md
e7a2007 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
d1064df 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
3c63959 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
33a49b7 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
b8e9efb 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
a9d5844 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/training.ipynb
66bab3d 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/data_generation_variant.ipynb
c99d5fd 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2
Update tutorials/data_generation_ppi.ipynb
ee2741d 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
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Update tutorials/data_generation_variant.ipynb
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Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
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Update tutorials/data_generation_variant.ipynb
5102d85 
Co-authored-by: Dani Bodor <d.bodor@esciencecenter.nl>
@gcroci2 gcroci2 requested a review from DaniBodor August 4, 2023 16:02
@gcroci2 gcroci2 mentioned this pull request Aug 4, 2023
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@gcroci2 gcroci2 linked an issue Aug 4, 2023 that may be closed by this pull request
Fix link in TUTORIAL.md #462
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@gcroci2 gcroci2 mentioned this pull request Aug 4, 2023
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@gcroci2 gcroci2 linked an issue Aug 4, 2023 that may be closed by this pull request
Add documentation for Variant queries #371
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DaniBodor
DaniBodor approved these changes Aug 10, 2023
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I think it's all fine. Minor suggestions.
The one thing that really confuses me is that you removed BA as a default target (see comment below).

@gcroci2 gcroci2 requested a review from DaniBodor August 11, 2023 10:33
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github-actions bot commented Aug 28, 2023

This PR is stale because it has been open for 14 days with no activity.

@github-actions github-actions bot added the stale issue not touched from too much time label Aug 28, 2023
@DaniBodor DaniBodor mentioned this pull request Aug 31, 2023
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@gcroci2 gcroci2 merged commit 4edc863 into main Sep 1, 2023
@gcroci2 gcroci2 deleted the 435_add_tutorials_variants_gcroci2 branch September 1, 2023 08:46
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Fix link in TUTORIAL.md Add tutorials for variants Add documentation for Variant queries

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