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dataset: DISEASES#39

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tristan-f-r merged 44 commits intomainfrom
diseases_dataset
Dec 26, 2025
Merged

dataset: DISEASES#39
tristan-f-r merged 44 commits intomainfrom
diseases_dataset

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@AMINOexe
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@AMINOexe AMINOexe commented Jul 29, 2025 •
edited by tristan-f-r
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added DISEASE db benchmarking

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agitter commented Jul 29, 2025

One quick general thing I noticed is that the macOS .DS_Store files are included. We should add a .gitignore pattern to exclude those from the repo.

@tristan-f-r tristan-f-r added the dataset Mutating datasets in any way. label Jul 29, 2025
@tristan-f-r tristan-f-r changed the title Diseases dataset dataset: diseases Jul 30, 2025
@tristan-f-r tristan-f-r changed the title dataset: diseases dataset: DISEASES Jul 30, 2025
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tristan-f-r requested changes Jul 30, 2025
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We can also drop dataPre.ipnyb once we transfer the comments over. I've gone in and committed some pathlib changes to make this correct regardless of CWD, as well as added some comments where I'm confident.

@tristan-f-r tristan-f-r mentioned this pull request Jul 30, 2025
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@tristan-f-r tristan-f-r mentioned this pull request Aug 10, 2025
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ntalluri commented Aug 11, 2025

Is there any information on how to use the scripts and the data? Something similar to Grace's Cell line ReadMe would be helpful.

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tristan-f-r commented Aug 11, 2025 •
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There isn't. I don't believe this even has a Snakefile attached, either. I wasn't able to go through the same documentation process as in #42 with this PR, so this is something to ask @AMINOexe for.

Also, my above review is stale: while I didn't ask about general code workings, there is a stable fetch.py attached now.

ntalluri
ntalluri reviewed Oct 24, 2025
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tristan-f-r and others added 24 commits December 15, 2025 05:57
@tristan-f-r
fix: create directories, make snakemake
e543755
@tristan-f-r
chore: drop unnecessary cmt
6921df5
@tristan-f-r
use csv instead of pickle, merge diseases yaml to dmmm yaml
bfa2fb6
@tristan-f-r
chore: mv around files, correctly use non-pickled file
0350891
@tristan-f-r
Merge branch 'main' into diseases_dataset
c273418
@tristan-f-r
chore: bump spras
96f01d4
@tristan-f-r
Merge branch 'main' into diseases_dataset
168f580
@tristan-f-r
feat: cache, databases
1117233
@tristan-f-r
fix: properly download cache items
728dbb6
@tristan-f-r
chore: cleanup
4f04bcf
@tristan-f-r
feat: consider aliases
fce53cb
@tristan-f-r
feat(inputs.py): drop use of STRING API
3b07532
@tristan-f-r
feat: use protein aliases for gold_standard
eba0fda
@tristan-f-r
fix: drop duplicates of non str_id subset
be5253f
@tristan-f-r
style: fmt
2846eb9
@tristan-f-r
chore: bump
21a6961
@tristan-f-r
fix: correct snakefile
775af24
@tristan-f-r
fix: preserve str_id
b1d4ced
@tristan-f-r
feat: setup biomart fetching
50b8aa4
@tristan-f-r
feat: use biomart instead of the gconvert wrapper
45b3304
@tristan-f-r
docs(biomart): provide context to biomart folder
964c3d9
@tristan-f-r
docs: more biomart
1a43d73
@tristan-f-r
config: correct dmmm prefix
5e85513
@tristan-f-r
chore: drop dataPreb.ipynb
832e773
tristan-f-r
tristan-f-r approved these changes Dec 26, 2025
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Merging this so I can use the new cache and databases files inside #41.

@tristan-f-r tristan-f-r merged commit 76f1bb6 into main Dec 26, 2025
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@tristan-f-r tristan-f-r deleted the diseases_dataset branch December 26, 2025 08:58
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@AMINOexe @agitter @ntalluri @tristan-f-r @annaritz