scverse/pertpy

View on GitHub

Single-cell perturbation analysis

Stars: 346
Forks: 67
Open beginner issues: 0
Indexed issues: 10
Avg merge: 1d 4h
Merged PRs (30d): 13

Dominant language: Python
License: MIT
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

10 open issues indexed

Remove anndata pin when 0.14.0 is released Open

scverse/pertpy#1071 · 1 assignee · Opened Aug 7, 2026
Multimodal perturbation readouts (Perturb-CITE-seq, Perturb-ATAC, multiome) Open

enhancement

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

scverse/pertpy#1039 · Opened Jul 7, 2026
Spatial perturbation analysis Open

enhancement

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

scverse/pertpy#1038 · Opened Jul 7, 2026
Experimental design & power analysis for perturbation screens Open

enhancement

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

scverse/pertpy#1037 · Opened Jul 7, 2026
Drug-discovery analyses: connectivity-map / signature reversal, synergy & dose-response, genetic interactions Open

enhancement

scverse/pertpy#1036 · 10 comments · 2 assignees · Opened Jul 7, 2026
Benchmarking & evaluation harness for perturbation prediction (baseline-aware) Open

enhancement

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

scverse/pertpy#1035 · Opened Jul 7, 2026
Response prediction: predict unseen perturbations & combinations (GEARS, CPA/chemCPA, biolord, FM embeddings) Open

enhancement

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

scverse/pertpy#1034 · Opened Jul 7, 2026
Move differential expression analysis to separate package Open

enhancement

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

scverse/pertpy#730 · 5 comments · 4 reactions · Opened Mar 19, 2025
Got an error when using 'random_forest_regressor' estimator Open

scverse/pertpy#655 · 5 comments · 1 assignee · Opened Jul 23, 2024
Add linear mixed effects model to DE interface Open

enhancement

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

scverse/pertpy#614 · 1 reaction · Opened May 27, 2024

scverse/pertpy

Get new issues in your inbox