Issues

• 10x MEX filter: chemistry key passed where Cell Ranger expects description, FDR falls back to 0.01

  PavlidisLab/Gemma#1700 · Filter by author rachadele opened on Oct 19, 2026

• Dataset samples endpoint returns null arrayDesign.taxon for Generic_mouse_ncbiIds

  rest-api
  PavlidisLab/Gemma#1699 · Filter by author rachadele opened on Oct 15, 2026
  1

• Single-cell sample with all-zero counts is loaded and exported (GSE214244.1, 12,803 empty cells)

  single cell
  PavlidisLab/Gemma#1698 · Filter by author rachadele opened on Oct 15, 2026
  1

• Bulk and single-cell transcriptome references are not synchronized (rat GRCr8 exposes the gap)

  PavlidisLab/Gemma#1695 · Filter by author ppavlidis opened on Sep 22, 2026

• truncated files are generated inconsistently when fresh annotation files are requested via the getPlatformAnnotations endpoint

  PavlidisLab/Gemma#1690 · Filter by author oganm opened on Sep 1, 2026

• resultSets/{resultSet} enpoint rounds p values too aggressively for the tsv output

  PavlidisLab/Gemma#1672 · Filter by author oganm opened on Jul 10, 2026

• CellXGene id realiance

  PavlidisLab/Gemma#1670 · Filter by author oganm opened on Jul 8, 2026
  1

• CellXGene import donor-id disambiguation

  PavlidisLab/Gemma#1669 · Filter by author oganm opened on Jul 8, 2026

• move quantileNormalize fix to basecode

  PavlidisLab/Gemma#1662 · Filter by author oganm opened on May 26, 2026

• API changes for curation agents

  g2-addressed
  PavlidisLab/Gemma#1651 · Filter by author oganm opened on May 6, 2026
  5

• Duplicate column name BioAssay Id=1577370 Name=C2A_neg - caudal ganglionic eminence derived GABAergic cortical interneuron

  g2-addressed
  Bug

  PavlidisLab/Gemma#1630 · Filter by author arteymix opened on Feb 27, 2026
  2

• Exception during index Merge operation

  g2-addressedhigh priority
  Bug

  PavlidisLab/Gemma#1629 · Filter by author arteymix opened on Feb 27, 2026
  3

  

• Failed to initialize Mammalian Phenotype Ontology

  g2-addressed
  Bug

  PavlidisLab/Gemma#1628 · Filter by author arteymix opened on Feb 27, 2026 · 1.32.7
  2

• Allow performing DEA on a subset of the samples

  enhancementg2-addressed
  Feature

  PavlidisLab/Gemma#1622 · Filter by author arteymix opened on Feb 20, 2026 · 1.32.7
  1

  

• java.util.NoSuchElementException when post-processing GSE221856.1

  g2-addressedhigh priority
  Bug

  PavlidisLab/Gemma#1620 · Filter by author cyan864 opened on Feb 19, 2026 · 1.32.7
  2

  

• Handle better experiments lacking a design or make it non-null

  databaseenhancementg2-addressedlow priority
  Feature

  PavlidisLab/Gemma#1618 · Filter by author arteymix opened on Feb 17, 2026 · 1.32.7
  2

  

• Provide prefix-aware completions for the CLI

  clienhancementg2-addressed
  Feature

  PavlidisLab/Gemma#1615 · Filter by author arteymix opened on Feb 15, 2026
  2

• Add a completion endpoint to the REST API

  g2-addressedrest-api
  Feature

  PavlidisLab/Gemma#1611 · Filter by author arteymix opened on Feb 10, 2026
  4

• Find ontology term by OBO IDs

  enhancementg2-addressed
  PavlidisLab/Gemma#1610 · Filter by author arteymix opened on Feb 10, 2026
  3

• Expose a special attribute for result sets to refer to the experiment or source experiment for subsets

  enhancementg2-addressedrest-api
  Feature

  PavlidisLab/Gemma#1601 · Filter by author arteymix opened on Jan 29, 2026
  2

• Creating an experimental factor is slow and sometimes fail

  g2-addressedhigh priorityperformance
  Bug

  PavlidisLab/Gemma#1599 · Filter by author arteymix opened on Jan 28, 2026 · 1.32.7
  3

• NullPointerException when searching datasets

  g2-addressedrest-api
  Bug

  PavlidisLab/Gemma#1587 · Filter by author arteymix opened on Jan 12, 2026 · 1.32.7
  2

• Improve tabular data and design files available for download

  g2-addressed
  Feature

  PavlidisLab/Gemma#1586 · Filter by author arteymix opened on Jan 10, 2026 · 1.33.0
  3

  

• Inserts are not properly ordered when populating number of cells

  g2-addressedlow priorityworkaroud
  Bug

  PavlidisLab/Gemma#1578 · Filter by author arteymix opened on Dec 15, 2025
  2

• Display the number of cells in more places

  g2-addressed
  Feature

  PavlidisLab/Gemma#1562 · Filter by author arteymix opened on Nov 20, 2025
  2