Skip to content

dataset: DISEASES #39

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
tristan-f-r merged 44 commits into from
Dec 26, 2025
Merged

dataset: DISEASES #39

tristan-f-r merged 44 commits into from
Dec 26, 2025

Conversation

@AMINOexe
Copy link
Contributor

@AMINOexe AMINOexe commented Jul 29, 2025 •
edited by tristan-f-r
Loading

added DISEASE db benchmarking

@agitter
Copy link
Collaborator

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
tristan-f-r
tristan-f-r requested changes Jul 30, 2025
View reviewed changes
Copy link
Contributor

@tristan-f-r tristan-f-r left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
Merged
@tristan-f-r tristan-f-r mentioned this pull request Aug 10, 2025
Open
@ntalluri
Copy link
Contributor

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.

@tristan-f-r
Copy link
Contributor

tristan-f-r commented Aug 11, 2025 •
edited
Loading

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
View reviewed changes
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
View reviewed changes
Copy link
Contributor

@tristan-f-r tristan-f-r left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
3 checks passed
@tristan-f-r tristan-f-r deleted the diseases_dataset branch December 26, 2025 08:58
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@agitter agitter agitter left review comments

@tristan-f-r tristan-f-r tristan-f-r approved these changes

+1 more reviewer

@ntalluri ntalluri ntalluri left review comments

Reviewers whose approvals may not affect merge requirements

Assignees

No one assigned

Labels

dataset Mutating datasets in any way.

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

6 participants

@AMINOexe @agitter @ntalluri @tristan-f-r @annaritz