Regulatory target prioritization by lizzyjoan · Pull Request #10 · lasseignelab/setbp1_hd

lizzyjoan · 2026-04-03T21:25:38Z

Summary

This analysis uses the SETBP1 curated targets (260403_setbp1_targets.csv), spatiotemporal coexpression (PR#9), and SETBP1-associated pathways (see manuscript draft ) to prioritize targets for downstream drug analysis

Author Checklist

This repository has a Lasseigne Lab ruleset configured.
See instructions here.
A singularity container has been created with all dependancies and the
cap_container command has been included in each script using a container.
All of the necessary scripts, dependencies, and inputs have been included
in this pull request.
Only files relevant to this change are included; no temporary, generated,
or unrelated files are part of this pull request. Use .gitignore to prevent
irrelevant files from accidentally being included.
Results have been reproduced and verified with lasseignelab and
default environments by running the job until two consecutive runs produce
the same results. Code comments (per script) have been added for
non-reproducible scripts. Include information about why the script is not
reproducible.
All automated code checks have passed. The "All checks have passed"
message should show in the GitHub pull request status box above the
"Merge pull request" button.
No merge conflicts exist. Merge conflicts are indicated by the "This
branch has conflicts that must be resolved" message in the GitHub pull
request status box above the "Merge pull request" button.
Primary and secondary reviewers have been requested to review this
pull request.

Self/Peer Review Checklist (Coding Guidelines)

Meaningful variable and function names
File header comments
Function comments
In-line comments summarize logical sections of code by concisely explaining
why, not what the code is doing. Avoid excessive or redundant commenting.
Random seed is set
Reasonable processing time for each job or script is specified
All outputs have been saved
Session info included in the scripts
Cross-reference the working draft of the paper
Confirm the code performs the intended analysis
Confirm the code reproduces the reported results

Setup

Ensure you have CAPTURE v1.0.0 with the cap version and cap update commands.
This PR depends on permutation analysis results from PR#9

cd $USER_SCRATCH/setbp1_hd
git checkout main
git pull

git checkout prioritize_targets
git pull origin prioritize_targets

Reproduce results

Run target prioritization script (should take > 5 min)

cap run -s batch src/permutation_analysis/04_job_prioritize.sh

Verification

cap verify verifications/permutations_prioritize.sh

Then check for any differences

git diff verifications/

This should return nothing, indicating no differences between outputs

…prioritize_targets Conflicts: src/permutation_analysis/prioritize_targets.R # # It looks like you may be committing a merge. # If this is not correct, please remove the file # .git/MERGE_HEAD # and try again. # Please enter the commit message for your changes. Lines starting # with '#' will be kept; you may remove them yourself if you want to. # An empty message aborts the commit. # On branch prioritize_targets # All conflicts fixed but you are still merging. # (use "git commit" to conclude merge) # # Changes to be committed: # # modified: config/environments/lasseignelab.sh # new file: data/260303_setbp1_targets.csv # deleted: data/setbp1_target_pathways.csv # deleted: results/permutation_analysis/SETBP1_target_exp_gtex_heatmap.png # deleted: results/permutation_analysis/SETBP1_temporal_trajectory.png # deleted: results/permutation_analysis/brainspan_age_donor_counts.png # renamed: results/permutation_analysis/metadata_development_windows.csv -> results/permutation_analysis/brainspan_metadata_dev_windows.csv # renamed: results/permutation_analysis/temporal_window_perm_stats.csv -> results/permutation_analysis/brainspan_permutation_stats.csv # renamed: results/permutation_analysis/temporal_window_gene_means.csv -> results/permutation_analysis/brainspan_window_gene_means.csv # deleted: results/permutation_analysis/devgtex_adult_permutations.rds # deleted: results/permutation_analysis/gtex_adult_permutations.rds # deleted: results/permutation_analysis/gtex_metadata_brain_regions.png # renamed: results/permutation_analysis/postnatal_gtex_permutation_results.csv -> results/permutation_analysis/gtex_permutation_results.csv # renamed: results/permutation_analysis/postnatal_gtex_sex_results.csv -> results/permutation_analysis/gtex_sex_wilcox_results.csv # deleted: results/permutation_analysis/gtex_stage_exp_boxplot.png # deleted: results/permutation_analysis/prenatal_postnatal_gene_means.csv # deleted: results/permutation_analysis/prenatal_postnatal_gene_median.csv # deleted: results/permutation_analysis/temporal_exp_trajectory.png # deleted: src/01_prioritized_targets_df.R # modified: src/figures/supp_figure_1.R # modified: src/permutation_analysis/01_fetch_temporal_exp.sh # modified: src/permutation_analysis/02_job_permutation.sh # modified: src/permutation_analysis/02_spatiotemporal_perm.R # modified: src/permutation_analysis/03_job_permutation.sh # modified: src/permutation_analysis/03_postnatal_development.R # deleted: src/permutation_analysis/job_prioritize_targets.sh # deleted: src/permutation_analysis/prioritize_targets.R # new file: verifications/permutations_fetchdata.out # new file: verifications/permutations_fetchdata.sh # new file: verifications/permutations_run.out # new file: verifications/permutations_run.sh #

github-actions · 2026-04-06T16:51:56Z

🦙 MegaLinter status: ⚠️ WARNING

Descriptor	Linter	Files	Errors	Elapsed time
⚠️ BASH	bash-exec	27	24	0.26s
✅ BASH	shellcheck	27	0	0.22s
⚠️ BASH	shfmt	27	19	0.02s
⚠️ MARKDOWN	markdownlint	2	13	0.52s
✅ MARKDOWN	markdown-link-check	2	0	3.03s
✅ MARKDOWN	markdown-table-formatter	2	0	0.22s
✅ R	lintr	13	0	9.6s

See detailed report in MegaLinter reports

You could have same capabilities but better runtime performances if you request a new MegaLinter flavor.

Click here to request the new flavor

…prioritize_targets

…ETBP1 pathways

…prioritize_targets

…hondrial/bioenergetic pathway evidence too limited)

…ize_targets

tsoelter

Outputs verify! 🎉

sashataluri

No issues with it. Looks great.

lizzyjoan added 6 commits April 1, 2026 11:14

update path for outputs

f26cbf6

update prioritization script names

8401a97

fix filenames and output filepaths

47805ff

filter for top 10% instead of top 25% coexpressed genes

0fbf54f

update prioritization with updated SETBP1 targets

893c69a

lizzyjoan added 9 commits April 6, 2026 14:01

updated pathways

dafdedc

Merge branch 'permutation' of github.com:lasseignelab/setbp1_hd into …

f3470a2

…prioritize_targets

update with PHAROS annotations

4995bbd

update SETBP1 relevant pathways

05d5e2a

filter prioritized targets by PHAROS druggability level and updated S…

00c91e9

…ETBP1 pathways

rename output files

17a117b

lint, style, and verify

4b16167

Merge branch 'permutation' of github.com:lasseignelab/setbp1_hd into …

32ac745

…prioritize_targets

update slurm resources requested

e9b5fd0

lizzyjoan requested review from sashataluri and tsoelter April 7, 2026 17:59

lizzyjoan added 4 commits April 7, 2026 13:39

prioritize by 3 core pathway modules with most direct evidence (mitoc…

2bba18c

…hondrial/bioenergetic pathway evidence too limited)

cleanup table (replace '_' with ' ' in GO terms)

f42d9bf

Merge branch 'main' of github.com:lasseignelab/setbp1_hd into priorit…

e07f612

…ize_targets

update verification

ededda6

lizzyjoan marked this pull request as ready for review April 10, 2026 15:06

tsoelter previously approved these changes Apr 10, 2026

View reviewed changes

Comment thread src/permutation_analysis/04_prioritize_targets.R Outdated

fix comments

be2a83c

lizzyjoan dismissed tsoelter’s stale review via be2a83c April 10, 2026 16:43

tsoelter self-requested a review April 10, 2026 17:17

tsoelter approved these changes Apr 10, 2026

View reviewed changes

sashataluri approved these changes Apr 13, 2026

View reviewed changes

lizzyjoan merged commit 1d412e0 into main Apr 14, 2026
1 check passed

lizzyjoan deleted the prioritize_targets branch April 14, 2026 14:20

Navigation Menu

Uh oh!

Regulatory target prioritization - #10

Regulatory target prioritization#10
lizzyjoan merged 20 commits into
mainfrom
prioritize_targets

lizzyjoan commented Apr 3, 2026 •

edited

Loading

Uh oh!

github-actions Bot commented Apr 6, 2026 •

edited

Loading

Uh oh!

tsoelter left a comment

Uh oh!

Uh oh!

sashataluri left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Uh oh!

Conversation

lizzyjoan commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

Author Checklist

Self/Peer Review Checklist (Coding Guidelines)

Setup

Reproduce results

Verification

Uh oh!

github-actions Bot commented Apr 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

🦙 MegaLinter status: ⚠️ WARNING

Uh oh!

tsoelter left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

sashataluri left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

lizzyjoan commented Apr 3, 2026 •

edited

Loading

github-actions Bot commented Apr 6, 2026 •

edited

Loading