Skip to content

fix: GeneSets bug#1232

Merged
kaloster merged 6 commits into
mainfrom
kaloster/fix-de-bug
Jul 9, 2025
Merged

fix: GeneSets bug#1232
kaloster merged 6 commits into
mainfrom
kaloster/fix-de-bug

Conversation

@kaloster

@kaloster kaloster commented Jul 9, 2025

Copy link
Copy Markdown
Contributor

Users reported issues where:

  • Gene list under GeneSets were not appearing when using Differential Expression feature
  • Genes are missing from gene search

Changes:

  • Updated Gene Expression logic to handle DE genesets while maintaining same functionality for user genesets
  • Updated max categories to avoid omitting genes from the list - previously capped at 1000

@kaloster kaloster requested review from Copilot and tihuan July 9, 2025 18:17

Copilot AI left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

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

Pull Request Overview

This PR addresses a bug in differential expression (DE) functionality by increasing the category limit and improving gene ID resolution logic. The changes focus on handling larger datasets and ensuring proper gene name/ID mapping when processing genesets.

  • Increased maximum categories limit from 1,000 to 30,000 to accommodate larger datasets
  • Enhanced gene ID resolution to handle cases where gene names may be stored as IDs
  • Improved gene name mapping to use the correct display name for genes

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File Description
server/default_config.py Increases max_categories from 1000 to 30000
client/src/components/RightSideBar/components/GeneExpression/GeneExpression.tsx Enhances gene ID/name resolution logic with fallback mechanisms

@kaloster kaloster force-pushed the kaloster/fix-de-bug branch from f0c9f5c to eae2be1 Compare July 9, 2025 19:03
@kaloster kaloster changed the title fix: DE bug fix: GeneSets bug Jul 9, 2025
@kaloster kaloster added the stack label Jul 9, 2025
@codecov

codecov Bot commented Jul 9, 2025

Copy link
Copy Markdown

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 0.00%. Comparing base (30d5e94) to head (f531f95).
Report is 1 commits behind head on main.

Additional details and impacted files
@@     Coverage Diff      @@
##   main   #1232   +/-   ##
============================
============================

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

@kaloster kaloster force-pushed the kaloster/fix-de-bug branch from da8ece8 to 2f9b69f Compare July 9, 2025 19:13
@kaloster kaloster force-pushed the kaloster/fix-de-bug branch from 2f9b69f to 3ef2abc Compare July 9, 2025 19:17
@kaloster kaloster force-pushed the kaloster/fix-de-bug branch 2 times, most recently from 3d6162a to 0915b7d Compare July 9, 2025 20:19
@kaloster kaloster force-pushed the kaloster/fix-de-bug branch from 0915b7d to da493ac Compare July 9, 2025 20:24
@kaloster kaloster requested a review from rainandbare July 9, 2025 21:48
@kaloster kaloster merged commit 43780a5 into main Jul 9, 2025
36 checks passed
@kaloster kaloster deleted the kaloster/fix-de-bug branch July 9, 2025 21:50
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants