scverse/scirpy

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A scanpy extension to analyse single-cell TCR and BCR data.

Stars: 265
Forks: 50
Open beginner issues: 0
Indexed issues: 35
Avg merge: 9d 9h
Merged PRs (30d): 4

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

35 open issues indexed

Split tutorials into "gallery" Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 48/100

scverse/scirpy#733 · Opened Jul 29, 2026
Fix test warnings Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/scirpy#731 · Opened Jul 27, 2026
representing spatial AIRR data in anndata/spatialdata Open

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

scverse/scirpy#719 · 3 comments · 1 reaction · Opened Jun 24, 2026
use scverse-misc for logging Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/scirpy#706 · Opened May 11, 2026
use scverse-misc for settings Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/scirpy#705 · Opened May 11, 2026
Handle sequences with different length in logoplots Open

good first issue

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/scirpy#691 · 1 comment · Opened Apr 29, 2026
New tutorial: query tetramer-staining datasets Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 54/100

scverse/scirpy#677 · 2 comments · Opened Feb 17, 2026
Index chain error after concatenating adatas Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/scirpy#648 · 4 comments · Opened Oct 1, 2025
Avoid GPL Dependencies as Hard Dependencies Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/scirpy#603 · 3 comments · Opened Mar 12, 2025
Add support for spot-based spatial data and bulk data Open

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

scverse/scirpy#583 · Opened Dec 16, 2024
Dealing with alleles and multiple gene calls Open

scverse/scirpy#561 · 8 comments · 1 assignee · Opened Oct 8, 2024
Refactor distance metric histogram Open

breaking-change

scverse/scirpy#548 · 1 assignee · Opened Aug 30, 2024
Community tutorial page Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

scverse/scirpy#495 · Opened Feb 28, 2024
Add the Morisita-Horn index for repertoire overlap similarity scores Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/scirpy#488 · 1 comment · Opened Jan 29, 2024
Can't save h5mu from Scirpy processed gex+bcr+tcr data if I copy airr into obs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/scirpy#434 · 3 comments · Opened Jul 19, 2023
Plot preview doesn't show in API docs Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/scirpy#429 · 2 comments · Opened Jul 5, 2023
In ir.pl.repertoire_overlap() function the `fraction` param is not working Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/scirpy#424 · 4 comments · Opened Jul 3, 2023
Refactor _get_color function to stop using private scanpy functions and to work with mudata Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/scirpy#388 · Opened Mar 29, 2023
Split IO into separate package Open

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

scverse/scirpy#385 · 2 comments · Opened Mar 16, 2023
clean up usage of _is_na, _is_true and _is_false Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/scirpy#380 · Opened Jan 29, 2023
antigen specificity prediction Open

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

scverse/scirpy#371 · 2 comments · Opened Oct 18, 2022
Autoencoder-based sequence embedding Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/scirpy#369 · 10 comments · Opened Oct 9, 2022
Speed up read_airr Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/scirpy#367 · 2 comments · Opened Oct 9, 2022
spatial airr data Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/scirpy#354 · 6 comments · Opened Jul 6, 2022
Why `clonotype_imbalance` is deprecated? Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

scverse/scirpy#330 · 5 comments · Opened Mar 30, 2022
Improve clonotype network plot with plotAtlas Open

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

scverse/scirpy#318 · 1 comment · Opened Jan 13, 2022
Plot overhaul Open

breaking-change

Difficulty 5/5 Over a week Newbie friendliness 15/100

scverse/scirpy#247 · 5 comments · Opened Mar 10, 2021
TCR sharing cluster plot Open

new-feature

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

scverse/scirpy#234 · Opened Jan 26, 2021
Refactoring group_abundance. Open

breaking-change

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/scirpy#232 · 3 comments · Opened Jan 13, 2021
Figure style breaks multi-panel plots. Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/scirpy#193 · Opened Oct 7, 2020
Refactor clonotype_imbalance Open

breaking-change good first issue

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/scirpy#160 · 3 comments · Opened Jun 4, 2020
Restructure repertoire overlap functions Open

breaking-change

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/scirpy#156 · Opened Jun 4, 2020
Clonotype overlap as Venn diagram? Open

new-feature

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/scirpy#55 · 1 comment · Opened Apr 9, 2020
Clonotype dotplot Open

new-feature

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

scverse/scirpy#52 · 2 comments · Opened Apr 9, 2020
Public and private epitopes Open

new-feature

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/scirpy#27 · 1 comment · Opened Apr 9, 2020

scverse/scirpy

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