List view

Add support for ordinal factors

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

low priority

Status: Open.

Feature

#1546 In PavlidisLab/Gemma;

· arteymix opened on Oct 31, 2025

Update HDF5 to 1.14

low priority

Status: Open.

Task

#1427 In PavlidisLab/Gemma;

· arteymix opened on Jun 18, 2025

Cell-level measurements

low priority

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

Status: Draft (not ready).

PavlidisLab/Gemmanumber 1375

#1375 In PavlidisLab/Gemma;

· arteymix opened on Apr 19, 2025

Allow statements in EE tags

annotations

enhancementEnhance the code or user experienceEnhance the code or user experience

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

Status: Open.

Feature

#1459 In PavlidisLab/Gemma;

· ppavlidis opened on Jul 4, 2025

Add outlier status to the Sample details table (curation)

enhancementEnhance the code or user experienceEnhance the code or user experience

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

low priority

Status: Open.

#1457 In PavlidisLab/Gemma;

· ppavlidis opened on Jul 3, 2025

Boxplot of cell-level expression by gene and contrast

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

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

Status: Open.

Feature

#1333 In PavlidisLab/Gemma;

· arteymix opened on Feb 8, 2025

Use a DatabaseEntryValueObject for dataset accession

cleanupCode reorganization and changes that should not impact functionalityCode reorganization and changes that should not impact functionality

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

Status: Open.

#450 In PavlidisLab/Gemma;

· arteymix opened on Oct 3, 2022

Add other accessions for ExpressionExperiment, BioAssay and BioMaterial

Status: Draft (not ready).

PavlidisLab/Gemmanumber 1471

#1471 In PavlidisLab/Gemma;

· arteymix opened on Aug 3, 2025

Remove old-style characteristics

cleanupCode reorganization and changes that should not impact functionalityCode reorganization and changes that should not impact functionality

Status: Open.

#929 In PavlidisLab/Gemma;

· arteymix opened on Nov 1, 2023

Create metadata endpoint

enhancementEnhance the code or user experienceEnhance the code or user experience

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

Status: Open.

Feature

#73 In PavlidisLab/Gemma;

· tesar-stepan opened on Dec 21, 2018

Support continuous cell-level characteristics

low priority

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

Status: Open.

Feature

#1372 In PavlidisLab/Gemma;

· arteymix opened on Apr 16, 2025

Add a compact bitmask PrimitiveType for efficiently storing data masks

low priority

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

Status: Open.

Feature

#1374 In PavlidisLab/Gemma;

· arteymix opened on Apr 18, 2025

Remove usages of SimpleFormController

enhancementEnhance the code or user experienceEnhance the code or user experience

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

spring-4Issues related to Spring 4Issues related to Spring 4

Status: Open.

#1172 In PavlidisLab/Gemma;

· arteymix opened on Jun 30, 2024

Identify factors that are automatically generated and can safely be deleted or re-created

Status: Open.

Feature

#1498 In PavlidisLab/Gemma;

· arteymix opened on Aug 26, 2025

Mark ExperimentalFactor as auto-generated

Status: Draft (not ready).

PavlidisLab/Gemmanumber 1499

#1499 In PavlidisLab/Gemma;

· arteymix opened on Aug 26, 2025

Set a User-Agent header when performing external HTTP requests

Status: Open.

Task

#1514 In PavlidisLab/Gemma;

· arteymix opened on Sep 16, 2025

Add a JSON representation for the experimental design endpoint

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

Status: Open.

Task

#1515 In PavlidisLab/Gemma;

· arteymix opened on Sep 17, 2025

Add single-cell fields to the search index

enhancementEnhance the code or user experienceEnhance the code or user experience

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

Status: Open.

Task

#1265 In PavlidisLab/Gemma;

· arteymix opened on Oct 23, 2024

Remove the legacy browser from the menu

Status: Open.

Task

#1494 In PavlidisLab/Gemma;

· arteymix opened on Aug 25, 2025

Read NCBI API key from NCBI_API_KEY

cliIssues affecting the CLIIssues affecting the CLI

enhancementEnhance the code or user experienceEnhance the code or user experience

low priority

Status: Open.

#1212 In PavlidisLab/Gemma;

· arteymix opened on Aug 27, 2024