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Allow performing DEA on a subset of the samples

enhancementEnhance the code or user experienceEnhance the code or user experience

Status: Open.

Feature

#1622 In PavlidisLab/Gemma;

· arteymix opened on Feb 20, 2026

Make the experimental design non-nullable (fix #1618)

Status: Open (in progress).

PavlidisLab/Gemmanumber 1621

#1621 In PavlidisLab/Gemma;

· arteymix opened on Feb 19, 2026

Failed to initialize Mammalian Phenotype Ontology

Status: Open.

Bug

#1628 In PavlidisLab/Gemma;

· arteymix opened on Feb 27, 2026

Splitting an experiment should be annotated with @Transactional

enhancementEnhance the code or user experienceEnhance the code or user experience

Status: Open.

#194 In PavlidisLab/Gemma;

· arteymix opened on Sep 29, 2021

AffyFromCel leaves stray "preferred" QTs

Status: Open.

Bug

#902 In PavlidisLab/Gemma;

· ppavlidis opened on Oct 13, 2023

Foreign key error when running affyFromCel

needs confirmationIssues that need to be confirmed or reliably reproducedIssues that need to be confirmed or reliably reproduced

Status: Open.

Bug

#1129 In PavlidisLab/Gemma;

· arteymix opened on May 16, 2024

"Needs attention" remains unchecked

low priority

regressionIndicate that something that used to work is presently brokenIndicate that something that used to work is presently broken

Status: Open.

Bug

#1301 In PavlidisLab/Gemma;

· xnrxng opened on Dec 3, 2024

Finding ontology terms via genes and GO matches produces too many results and is very slow

performance

Status: Open.

Bug

#1348 In PavlidisLab/Gemma;

· arteymix opened on Apr 1, 2025

FVs are re-used when pre-populating a factor

needs confirmationIssues that need to be confirmed or reliably reproducedIssues that need to be confirmed or reliably reproduced

Status: Open.

Bug

#1358 In PavlidisLab/Gemma;

· arteymix opened on Apr 14, 2025

Datasets with continuous factors cannot be split

Status: Open.

Bug

#1382 In PavlidisLab/Gemma;

· arteymix opened on Apr 25, 2025

Failed to find date when extracting Affy metadata for GSE202043

needs confirmationIssues that need to be confirmed or reliably reproducedIssues that need to be confirmed or reliably reproduced

Status: Open.

Bug

#1387 In PavlidisLab/Gemma;

· arteymix opened on May 6, 2025

affyFromCel failed: LazyInitializationException: failed to lazily initialize a collection of role:

high priorityIssues that require immediate attentionIssues that require immediate attention

Status: Open.

Bug

#1418 In PavlidisLab/Gemma;

· arteymix opened on Jun 11, 2025

Various GUI fixes

guiIssues or pull requests involving the Web UIIssues or pull requests involving the Web UI

Status: Open.

Task

#1444 In PavlidisLab/Gemma;

· arteymix opened on Jun 21, 2025

Cannot read properties of undefined (reading 'label')]

guiIssues or pull requests involving the Web UIIssues or pull requests involving the Web UI

Status: Open.

Bug

#1448 In PavlidisLab/Gemma;

· arteymix opened on Jun 27, 2025

Diff ex "pie chart" doesn't indicate the threshold is a qvalue

guiIssues or pull requests involving the Web UIIssues or pull requests involving the Web UI

low priority

minor

Status: Open.

Bug

#1458 In PavlidisLab/Gemma;

· ppavlidis opened on Jul 4, 2025

Cannot delete or update a parent row: a foreign key constraint fails

Status: Open.

Bug

#1497 In PavlidisLab/Gemma;

· arteymix opened on Aug 26, 2025

OverlappingFileLockException when donloading processed data

needs confirmationIssues that need to be confirmed or reliably reproducedIssues that need to be confirmed or reliably reproduced

Status: Open.

Bug

#1524 In PavlidisLab/Gemma;

· arteymix opened on Oct 5, 2025

Single-cell datasets with a biomaterial hierarchy cannot be deleted

high priorityIssues that require immediate attentionIssues that require immediate attention

single cellIssues related to single-cell data supportIssues related to single-cell data support

Status: Open.

Bug

#1530 In PavlidisLab/Gemma;

· arteymix opened on Oct 8, 2025

Adjust how blacklisted entities are displayed

guiIssues or pull requests involving the Web UIIssues or pull requests involving the Web UI

minor

Status: Open.

Bug

#1535 In PavlidisLab/Gemma;

· arteymix opened on Oct 25, 2025

Prevent more than one CTA to be marked as preferred

single cellIssues related to single-cell data supportIssues related to single-cell data support

Status: Open.

Bug

#1538 In PavlidisLab/Gemma;

· arteymix opened on Oct 28, 2025

LazyInitializationException when attempting to split a dataset with other parts

Status: Open.

Bug

#1549 In PavlidisLab/Gemma;

· arteymix opened on Nov 4, 2025

NullPointerException when searching datasets

rest-apiIssues or pull requests involving the RESTful APIIssues or pull requests involving the RESTful API

Status: Open.

Bug

#1587 In PavlidisLab/Gemma;

· arteymix opened on Jan 12, 2026

Creating an experimental factor is slow and sometimes fail

high priorityIssues that require immediate attentionIssues that require immediate attention

performance

Status: Open.

Bug

#1599 In PavlidisLab/Gemma;

· arteymix opened on Jan 28, 2026

Lazy init exception when recreating the cell type factor from the GUI

guiIssues or pull requests involving the Web UIIssues or pull requests involving the Web UI

high priorityIssues that require immediate attentionIssues that require immediate attention

Status: Open.

Bug

#1608 In PavlidisLab/Gemma;

· arteymix opened on Feb 7, 2026

ClientAbortException are not suppressed in error logs for the REST API

rest-apiIssues or pull requests involving the RESTful APIIssues or pull requests involving the RESTful API

Status: Open.

Bug

#1616 In PavlidisLab/Gemma;

· arteymix opened on Feb 15, 2026