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Pull requests: PavlidisLab/Gemma

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Pull requests list

Bump launch-editor from 2.9.1 to 2.14.1 in /gemma-web/src/main/webapp dependencies Pull requests that update a dependency file javascript Pull requests that update javascript code minor
#1665 opened Jun 18, 2026 by dependabot Bot Loading…
Bump shell-quote from 1.8.1 to 1.8.4 in /gemma-web/src/main/webapp dependencies Pull requests that update a dependency file javascript Pull requests that update javascript code
#1664 opened Jun 9, 2026 by dependabot Bot Loading…
Quality of life changes
#1663 opened Jun 8, 2026 by oganm Member • Draft
add path to hdf5 path in build process to allow easier testing
#1642 opened Mar 12, 2026 by oganm Member • Draft
2
Allow DEA to be performed on a subset of the samples
#1627 opened Feb 24, 2026 by arteymix Collaborator Loading…
@oganm
18
Allow using any supported identifier when linting ACLs
#1626 opened Feb 23, 2026 by arteymix Collaborator Loading…
Make the experimental design non-nullable (fix #1618)
#1621 opened Feb 19, 2026 by arteymix Collaborator Loading… 1.32.7
1
@arteymix
1
Add support for filtering ACLs using subqueries
#1617 opened Feb 15, 2026 by arteymix Collaborator • Draft 1.33.0
1
Improvement for deployment script
#1614 opened Feb 14, 2026 by arteymix Collaborator • Draft
2 tasks
@arteymix
6
hiding expression and qc windows when no data is present
#1607 opened Feb 5, 2026 by oganm Member Loading…
3
Improvements for ACL advice
#1600 opened Jan 28, 2026 by arteymix Collaborator • Draft 1.33.0
1
Improve dataset splitting enhancement Enhance the code or user experience testing Feature or fix is being tested
#1589 opened Jan 14, 2026 by arteymix Collaborator Loading… 1.32.7
1
2
Reapply "More improvements for data matrices"
#1579 opened Dec 17, 2025 by arteymix Collaborator Loading…
1
Feature improve detection of experiment type
#1543 opened Oct 30, 2025 by arteymix Collaborator • Draft
Add a basic data processing report enhancement Enhance the code or user experience
#1529 opened Oct 7, 2025 by arteymix Collaborator • Draft 1.33.0
Prototype for loading cell-by-gene matrices low priority
#1525 opened Oct 6, 2025 by arteymix Collaborator • Draft
3 tasks
1
Mark ExperimentalFactor as auto-generated
#1499 opened Aug 26, 2025 by arteymix Collaborator • Draft 1.33.0
1
Bump org.apache.commons:commons-lang3 from 3.14.0 to 3.18.0 dependencies Pull requests that update a dependency file java Pull requests that update java code minor
#1480 opened Aug 5, 2025 by dependabot Bot Loading…
Bump commons-fileupload:commons-fileupload from 1.5 to 1.6.0 dependencies Pull requests that update a dependency file java Pull requests that update java code minor
#1478 opened Aug 5, 2025 by dependabot Bot Loading…
Single-cell batch correction
#1474 opened Aug 3, 2025 by arteymix Collaborator • Draft
5 tasks
1
1
Add other accessions for ExpressionExperiment, BioAssay and BioMaterial
#1471 opened Aug 3, 2025 by arteymix Collaborator • Draft 1.33.0
1
Cell-level measurements low priority single cell Issues related to single-cell data support
#1375 opened Apr 19, 2025 by arteymix Collaborator • Draft
4 of 9 tasks
1.33.0
2
2
Add support for loading simple cell type annotations from GEO supplem…
#1311 opened Dec 20, 2024 by arteymix Collaborator • Draft
Add a utility to create a SSH tunnel for the database
#1237 opened Sep 29, 2024 by arteymix Collaborator Loading…
4
Replace usages of SimpleFormController with annotation-based endpoints
#1173 opened Jul 2, 2024 by arteymix Collaborator • Draft
1
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