IGS/gEAR

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The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

Stars: 22
Forks: 6
Open beginner issues: 0
Indexed issues: 239
Avg merge: 2m
Merged PRs (30d): 8

Dominant language: Jupyter Notebook
License: AGPL-3.0
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

239 open issues indexed

Multigene Curator - Heatmaps still aggregate when matrixplot=false in API call Open

Page: multigene curator

IGS/gEAR#1324 · 1 comment · 1 assignee · Opened Sep 18, 2026
Dataset uploads - Enforcement of character limits in metadata HTML Open

data issues Page: dataset uploader

IGS/gEAR#1323 · 1 assignee · Opened Sep 14, 2026
Spatial - trigger background image caching after upload. Open

spatial

IGS/gEAR#1319 · 1 assignee · Opened Sep 9, 2026
Color scale doesn't match UMAP Dynamic Expression values Open

Page: single gene curator

IGS/gEAR#1313 · 1 assignee · Opened Aug 19, 2026
Spatial viewer - Add flip-x and flip-y functions for spatial plots Open

spatial

IGS/gEAR#1301 · 2 comments · 1 assignee · Opened Jul 22, 2026
Spatial Uploads - Accept precomputed UMAP coordinates Open

Page: dataset uploader spatial

IGS/gEAR#1298 · 1 comment · 1 assignee · Opened Jul 21, 2026
NeMO Analytics download .h5ad file format Open

IGS/gEAR#1297 · 11 comments · 1 assignee · Opened Jul 15, 2026
Create landing page for Pou3f4 project Open

IGS/gEAR#1288 · 3 comments · 1 assignee · Opened Jun 15, 2026
Start writing gEAR 2.0 paper text Open

IGS/gEAR#1286 · 1 comment · 1 assignee · Opened Jun 10, 2026
Gene List Manager - use genes as search terms to find lists Open

Page: gene list manager

IGS/gEAR#1284 · 1 assignee · Opened Jun 9, 2026
Add a more formal public gEAR API Open

IGS/gEAR#1279 · 1 comment · 2 assignees · Opened Jun 4, 2026
Update get help button to be built off a config Open

enhancement

IGS/gEAR#1255 · 1 assignee · Opened Apr 27, 2026
calculating and saving gene lists from the comparison tool Open

bug High Priority

IGS/gEAR#1253 · 1 comment · 2 assignees · Opened Apr 24, 2026
Make pip-audit part of testing / build process Open

IGS/gEAR#1241 · 2 comments · 1 assignee · Opened Apr 10, 2026
Add an analytics page Open

enhancement in_progress

IGS/gEAR#1236 · 3 comments · 1 assignee · Opened Mar 27, 2026
Track permalink entries Open

IGS/gEAR#1219 · 1 comment · 1 assignee · Opened Mar 24, 2026
Requirements gathering for exporting to cellxgene Open

3rd-party tool

IGS/gEAR#1192 · 1 comment · 1 assignee · Opened Feb 17, 2026
User request: Add ability to follow users and get notifications when they add datasets Open

user request

Difficulty 5/5 Over a week Newbie friendliness 25/100

IGS/gEAR#1189 · Opened Feb 7, 2026
Gosling - Save user session Open

gosling

IGS/gEAR#1187 · 1 comment · 1 assignee · Opened Feb 4, 2026
API for data download Open

good first issue

IGS/gEAR#1176 · 3 comments · 1 assignee · Opened Jan 23, 2026
Load new PatchSeq dataset in gEAR Open

2

IGS/gEAR#1171 · 1 assignee · Opened Jan 21, 2026
Min - Max Expression values Open

Page: multigene curator Page: search display pages Page: single gene curator

IGS/gEAR#1166 · 2 comments · 1 assignee · Opened Jan 14, 2026
Curators - Various customization features Open

Low Priority Page: multigene curator Page: single gene curator

IGS/gEAR#1154 · 1 assignee · Opened Nov 12, 2025
Option to collapse entire functional annotation Open

Page: search display pages

IGS/gEAR#1149 · 1 assignee · Opened Oct 31, 2025
Download expression values from multigene displays Open

good first issue Page: multigene curator user request

IGS/gEAR#1148 · 1 comment · 1 assignee · Opened Oct 30, 2025
Migrate from diffxpy to PyDESeq2 Open

3rd-party tool good first issue Low Priority Page: multigene curator

IGS/gEAR#1146 · 3 comments · 1 assignee · Opened Oct 26, 2025
move projection outputs into "cached" directory Open

code cleanup projectR

IGS/gEAR#1143 · 1 assignee · Opened Oct 22, 2025
Better control user-submitted library_strategy values Open

IGS/gEAR#1142 · 2 comments · 1 assignee · Opened Oct 17, 2025
Evaluate how we're handling individual datasets vs collections in the selector Open

IGS/gEAR#1135 · 1 assignee · Opened Oct 7, 2025
Add subsampling to volcano and quadrant plots Open

Page: multigene curator

IGS/gEAR#1132 · 1 comment · 1 assignee · Opened Sep 25, 2025
Associate Professor Open

question site_comment

IGS/gEAR#1126 · 1 comment · 2 assignees · Opened Sep 15, 2025
Implement Jupyter notebook integration Open

IGS/gEAR#1115 · 1 comment · 1 assignee · Opened Aug 21, 2025
gEAR citation inspiration page Open

documentation enhancement

IGS/gEAR#1101 · 1 assignee · Opened Jul 18, 2025
Create user story videos Open

documentation enhancement

IGS/gEAR#1100 · 1 assignee · Opened Jul 18, 2025
First dataset missing analysis in Vestibular profile Open

bug data issues

IGS/gEAR#1099 · 1 comment · 1 assignee · Opened Jul 18, 2025
add new meta data elements to gene lists restricting the possible projection methods that can be used with it Open

High Priority projectR

IGS/gEAR#1098 · 9 comments · 1 assignee · Opened Jul 15, 2025
(Displays blocking annotation loading) Deafness Gene Annotation is buggy Open

Page: search display pages

IGS/gEAR#1096 · 7 comments · 1 assignee · Opened Jul 14, 2025
Separate expression and continuous annotation colorings in scanpy plots Open

Low Priority Page: single gene curator

IGS/gEAR#1091 · 3 comments · 1 assignee · Opened Jul 10, 2025
Preprocessing steps for cochleae datasets Open

question

IGS/gEAR#1076 · 1 assignee · Opened Jun 10, 2025
If z-scoring is enabled for projection, allow users to filter low-expression genes Open

projectR

IGS/gEAR#1073 · 5 comments · 1 assignee · Opened Jun 9, 2025
find gene co-expression Open

IGS/gEAR#1069 · 1 comment · 1 assignee · Opened Jun 2, 2025
TCGA HPV Negative OC Open

IGS/gEAR#1064 · 3 comments · 2 assignees · Opened May 27, 2025
Add gene information for Xenium and other probe-based spatial platforms Open

spatial

IGS/gEAR#1048 · 1 assignee · Opened Apr 22, 2025
Add support for secondary annotation assignment based on projectR output Open

projectR

IGS/gEAR#1047 · 2 comments · 1 assignee · Opened Apr 17, 2025
Allow users to filter user history table on favorites Open

good first issue

IGS/gEAR#1046 · 1 assignee · Opened Apr 17, 2025
Allow users to 'favorite' dataset collections Open

good first issue

IGS/gEAR#1045 · 1 assignee · Opened Apr 17, 2025
Better explanation elements on gene list search widget Open

enhancement

IGS/gEAR#1038 · 3 comments · 1 assignee · Opened Apr 11, 2025
Make basic/advanced dataset search widget Open

IGS/gEAR#1037 · 1 comment · 1 assignee · Opened Apr 11, 2025
Uploader: Gracefully handle error when tarball fails to extract Open

bug dataset uploading

IGS/gEAR#1033 · 1 assignee · Opened Apr 3, 2025
Decouple services out of the Apache "API" process Open

enhancement Low Priority

IGS/gEAR#1022 · 1 comment · 1 assignee · Opened Mar 21, 2025

IGS/gEAR

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