scverse/scanpy

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Single-cell analysis in Python. Scales to >100M cells.

Stars: 2.6k
Forks: 779
Open beginner issues: 4
Indexed issues: 444
Avg merge: 1d 4h
Merged PRs (30d): 27

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue help wanted

Beginner friendly Everything

Open All

444 open issues indexed

`highly_variable_genes` with `batch_key` and `subset=True` keeps the wrong genes when `n_top_genes` is not set Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

scverse/scanpy#4370 · Opened Sep 17, 2026
`anndata.acc` based API for `obs_df`,`var_df` Open

Area – API

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

scverse/scanpy#4360 · Opened Sep 11, 2026
`calculate_qc_metrics(use_raw=True)` labels `.raw`'s matrix with `adata.var` Open

Difficulty 4/5 3-5 days Newbie friendliness 58/100

scverse/scanpy#4347 · Opened Sep 6, 2026
The `.uns` output for `scanpy.pp.highly_variable_genes` is not documented Open

Triage 🩺

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/scanpy#4341 · Opened Sep 3, 2026
`rank_genes_groups(method="t-test", mean_in_log_space=False)` runs the t-test on exponentiated values Open

Triage 🩺

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/scanpy#4336 · Opened Sep 2, 2026
sc.external.exporting.cellbrowser: cellbrowser_raw_data\sample_colors.tsv does not exist, skipping it An exception has occurred, use %tb to see the full traceback. Open

Triage 🩺

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

scverse/scanpy#4335 · Opened Sep 2, 2026
`anndata.acc` replacement for functions taking `obsm`, `layer`, … Open

Area – API

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

scverse/scanpy#4334 · Opened Sep 1, 2026
sc.pl.paga raises TypeError when cax is passed with multiple colors Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

scverse/scanpy#4318 · Opened Aug 22, 2026
Split up rank_genes_groups Open

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

scverse/scanpy#4305 · Opened Aug 18, 2026
Pre 2.0 janitor work Open

Area - Documentation 📒 Area – Performance 🐌 Area – Preprocessing 🧼

scverse/scanpy#4286 · 1 assignee · Opened Aug 10, 2026
log1p warning when modifying several layers Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/scanpy#4285 · 2 comments · Opened Aug 7, 2026
pp.regress_out returns wrong residuals when a covariate barely varies Open

scverse/scanpy#4280 · 1 assignee · Opened Aug 5, 2026
Investigate our neighbors algorithm choice Open

Area - Topology 🍩

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

scverse/scanpy#4131 · 15 comments · Opened May 19, 2026
wilcoxon DE, vs_all_perturbed Open

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

scverse/scanpy#4114 · 14 comments · Opened May 8, 2026
Investigate `networkit` (for `leiden` implementation) Open

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

scverse/scanpy#4110 · 4 comments · Opened May 7, 2026
Automatically using Dask for large datasets when necessary Open

Area - Out of core 💾

scverse/scanpy#4095 · 14 comments · 3 assignees · Opened Apr 28, 2026
`sc.get.aggregate` memory leak for Dask array Open

Area - Out of core 💾

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

scverse/scanpy#4074 · Opened Apr 18, 2026
Add `layer` parameter to `read_10x_*` functions Open

Area - IO

scverse/scanpy#4071 · 1 comment · 1 assignee · Opened Apr 17, 2026
modernize datasets Open

Area - Datasets

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

scverse/scanpy#4044 · Opened Apr 9, 2026
Opinionated defaults for 2.0 Open

Area – API

scverse/scanpy#4008 · 5 comments · 1 assignee · Opened Mar 23, 2026
`anndata.acc` based API Open

Area – API

scverse/scanpy#4007 · 5 comments · 1 assignee · Opened Mar 23, 2026
seaborn is broken with pandas 3: Violin plots squished, points misaligned Open

Area - Plotting 🌺 Upstream

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

scverse/scanpy#3991 · 2 comments · Opened Feb 26, 2026
Mislocation of colorbar legend by `sc.pl.scatter` Open

Area - Plotting 🌺

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

scverse/scanpy#3963 · Opened Jan 30, 2026
Add Poisson Gene Selection to HVG Open

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

scverse/scanpy#3956 · 1 reaction · Opened Jan 26, 2026
[RFC] Refactoring Scanpy's Numba Backend: C-Style Kernel Layer & Biology-Optimized Sparse Matrices Open

scverse/scanpy#3944 · 3 comments · 1 assignee · Opened Jan 12, 2026
Integration Testing CI Test Failure on python 3.13 Open

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

scverse/scanpy#3935 · Opened Jan 7, 2026
[RFC] Proposal: Architecture Modernization – Native Kernels, Model Hub & Lazy Dependencies Open

Area – Performance 🐌 Needs info❔

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

scverse/scanpy#3934 · 8 comments · Opened Dec 24, 2025
Order of pts and pts_rest in rank_genes_groups results doesn't match other fields in adata.uns["rank_genes_groups"] Open

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

scverse/scanpy#3930 · Opened Dec 22, 2025
Add TAU as an optional clustering method in Scanpy Open

Area - Community

Difficulty 5/5 Over a week Newbie friendliness 45/100

scverse/scanpy#3919 · 14 comments · Opened Dec 15, 2025
`pp.regress_out` fails with to many CPU-Cores Open

scverse/scanpy#3910 · 1 assignee · Opened Dec 11, 2025
Exposing some functions `squidpy` uses Open

Area – API

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

scverse/scanpy#3891 · Opened Nov 12, 2025
Highly Variable Genes Selection using CSC `dask` Open

Area - Out of core 💾 Area – Performance 🐌

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

scverse/scanpy#3862 · 1 comment · 1 reaction · Opened Oct 30, 2025
Implementation of `sc.tl.score_genes` doesn't match reference Open

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

scverse/scanpy#3845 · 2 comments · Opened Oct 23, 2025
Support values_to_plot in pl.rank_genes_groups_matrixplot and pl.rank_genes_groups_heatmap (parity with dotplot) Open

Area - Plotting 🌺

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/scanpy#3842 · 1 comment · Opened Oct 21, 2025
Regressing out variables in pearson residual normalization (SCTransform) Open

Needs info❔

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

scverse/scanpy#3838 · 1 comment · Opened Oct 20, 2025
Improve flexibility of `sc.pp.scrublet()` Open

Needs info❔

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

scverse/scanpy#3837 · 6 comments · Opened Oct 17, 2025
Export more types Open

Area – API

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

scverse/scanpy#3826 · 3 comments · Opened Oct 2, 2025
Apple Silicon: Accelerate or openBLAS for Numpy Open

Question

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

scverse/scanpy#3823 · 2 comments · Opened Sep 30, 2025
Unexpected number of non-zero distances when running `sc.pp.neighbors` with `transformer="pynndescent"` Open

Area - Topology 🍩

Difficulty 3/5 1-2 days Newbie friendliness 62/100

scverse/scanpy#3809 · 5 comments · Opened Sep 21, 2025
Custom neighbor transformers with variable neighbor count <= k fail Open

Area - Topology 🍩

Difficulty 4/5 3-5 days Newbie friendliness 55/100

scverse/scanpy#3806 · 1 comment · Opened Sep 19, 2025
Inconsistency of `basis` argument in plotting functions Open

Area - Plotting 🌺

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

scverse/scanpy#3803 · 1 comment · Opened Sep 18, 2025
replace remaining utils with fast-array-utils Open

Development Process 🚀

scverse/scanpy#3784 · 1 assignee · Opened Sep 4, 2025
sc.pp.scale changes adata.raw.X Open

Needs info❔

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

scverse/scanpy#3756 · 4 comments · Opened Jul 31, 2025
Don’t create AnnData objects with duplicate var/obs names in sc.datasets Open

breaking change ‼️

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

scverse/scanpy#3729 · Opened Jul 22, 2025
Column-wise `dask` `map_blocks` Open

Meta

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

scverse/scanpy#3723 · Opened Jul 21, 2025
Refactor `BasePlot` not to create a dataframe representation of the data Open

Area - Plotting 🌺 Area – Performance 🐌 good first issue

scverse/scanpy#3718 · 3 comments · 1 assignee · Opened Jul 18, 2025
sc.pl.dotplot is surprisingly ineffective for subsets of data Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/scanpy#3717 · 3 comments · Opened Jul 17, 2025
Investigate IRLBA Open

scverse/scanpy#3673 · 1 assignee · Opened Jun 6, 2025
Error when running sc.tl.rank_genes_groups Open

Needs info❔

Difficulty 4/5 3-5 days Newbie friendliness 20/100

scverse/scanpy#3671 · 2 comments · Opened Jun 6, 2025
Plotting a subset of the data with a dendrogram in e.g. dotplot should retain the dendrogram ordering Open

Area - Plotting 🌺

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

scverse/scanpy#3668 · 1 comment · Opened Jun 4, 2025

scverse/scanpy

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