Owner

scverse

43 indexed repositories · View on GitHub

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

Python · 2562 stars
scvi-tools
Deep probabilistic analysis of single-cell and spatial omics data

Python · 1695 stars
gget
🧬 gget enables efficient querying of genomic reference databases

Python · 1199 stars
anndata
Annotated data.

Python · 773 stars
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Python · 761 stars
squidpy
Spatial Single Cell Analysis in Python

Python · 598 stars
cellrank
CellRank: dynamics from multi-view single-cell data

Python · 456 stars
spatialdata
An open and interoperable data framework for spatial omics data

Python · 394 stars
rapids-singlecell
rapids-singlecell: GPU-accelerated framework for scRNA analysis

Python · 394 stars
pertpy
Single-cell perturbation analysis

Python · 345 stars
SnapATAC2
Single-cell epigenomics analysis tools

Python · 323 stars
liana
LIANA+: an all-in-one framework for cell-cell communication

Python · 315 stars
decoupler
Python package to perform enrichment analysis from omics data.

Python · 294 stars
muon
muon is a multimodal omics Python framework

Python · 279 stars
scirpy
A scanpy extension to analyse single-cell TCR and BCR data.

Python · 265 stars
anndataR
AnnData interoperability in R

R · 196 stars
mudata
Multimodal Data (.h5mu) implementation for Python

Python · 134 stars
spatialdata-io

Python · 103 stars
napari-spatialdata
Interactive visualization of spatial omics data

Python · 90 stars
cookiecutter-scverse
Cookiecutter template for scverse

Python · 89 stars
23 more repositories live on View on GitHub

Beginner friendly Everything

Open All

Some bugs I found while reviewing a PR Open

bug

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

scverse/annbatch#278 · Opened Sep 19, 2026
Why does fau need to know about numba internals for thread layer Open

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

scverse/fast-array-utils#215 · Opened Sep 18, 2026
Document each shipped dataset: derived columns, stats, and the scripts that rebuild it Open

documentation

Difficulty 4/5 Over a week Newbie friendliness 45/100

scverse/mantispy#74 · Opened Sep 18, 2026
ECOD aggregates as pyod does, not as the paper's Algorithm 1 Open

question

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

scverse/mantispy#72 · Opened Sep 18, 2026
Cell-resolution tests treat cells within a well as independent replicates Open

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

scverse/mantispy#68 · Opened Sep 18, 2026
transform_grouped reads the whole matrix to size its output, defeating the backed path Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

scverse/mantispy#67 · Opened Sep 18, 2026
Cross-fit the hit-calling covariance instead of splitting the controls in half Open

enhancement

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

scverse/mantispy#64 · Opened Sep 18, 2026
read_export cannot link objects that share a child instead of a parent Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 64/100

scverse/mantispy#61 · Opened Sep 18, 2026
np.errstate does not suppress numpy's all-NaN RuntimeWarnings in pp/_select.py Open

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

scverse/mantispy#57 · Opened Sep 17, 2026
pl.transport raises IndexError on an empty transport table Open

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

scverse/mantispy#55 · Opened Sep 17, 2026
pl.control_drift raises a bare IndexError at n_components=1 Open

Difficulty 1/5 Under an hour Newbie friendliness 90/100

scverse/mantispy#54 · Opened Sep 17, 2026
Add an iLISI and silhouette equivalence test against scib-metrics Open

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

scverse/mantispy#53 · Opened Sep 17, 2026
Migrate pp.harmony to scanpy's core harmony_integrate once 1.13 is stable Open

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

scverse/mantispy#52 · Opened Sep 17, 2026
`ClassSampler` undersamples longer runs and doesn't sample proportionally by run length Open

bug

scverse/annbatch#273 · 1 assignee · Opened Sep 17, 2026
Add cross-reference roles, admonitions and a standard page header Open

documentation

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

scverse/mantispy#48 · Opened Sep 17, 2026
Raise figure density in the tutorials Open

documentation

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

scverse/mantispy#47 · Opened Sep 17, 2026
Replace dict-literal result cells in the tutorials Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 65/100

scverse/mantispy#46 · Opened Sep 17, 2026
Split documentation into Tutorials, Examples and Pitfalls Open

documentation

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

scverse/mantispy#45 · Opened Sep 17, 2026
Tutorial index is a bare toctree; landing page is the README Open

documentation

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

scverse/mantispy#43 · Opened Sep 17, 2026
Tutorial prose refers to warnings the docs build strips Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 68/100

scverse/mantispy#42 · Opened Sep 17, 2026
Private symbols are imported in the published tutorials Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 65/100

scverse/mantispy#38 · Opened Sep 17, 2026
No public way to stamp a hand-built AnnData Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 68/100

scverse/mantispy#37 · Opened Sep 17, 2026
Publish to PyPI and submit to scverse ecosystem-packages Open

enhancement

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

scverse/mantispy#36 · Opened Sep 17, 2026
More `jit` options, specifically `nogil=True` on the serial kernels Open

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

scverse/fast-array-utils#213 · 4 comments · Opened Sep 17, 2026
`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
TOTALVI.get_normalized_expression omits learned protein capture efficiency Open

bug

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

scverse/scvi-tools#4022 · Opened Sep 16, 2026
Visium HD: empty `dataset_id` default produces an unnamed coordinate system that napari-spatialdata can't select Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 58/100

scverse/spatialdata-io#422 · Opened Sep 16, 2026
Outline color palette is ignored in `render_shapes` if no color is passed Open

bug

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

scverse/spatialdata-plot#777 · Opened Sep 16, 2026
Integration Testing CI Test Failure on python 3.12 Open

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

scverse/SnapATAC2#501 · Opened Sep 16, 2026
Bugs and problems in calculate_niche and in unreleased main. Open

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

scverse/squidpy#1293 · Opened Sep 15, 2026
Group modules in TOC Open

scverse/mantispy#27 · 1 assignee · Opened Sep 14, 2026
Use new annbatch/pertpy/etc doc style Open

scverse/mantispy#23 · 1 comment · 1 assignee · Opened Sep 14, 2026
Add logo Open

scverse/mantispy#22 · 1 assignee · Opened Sep 14, 2026
Large Cell Painting Gallery accessions in mantispy.ds Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/mantispy#21 · Opened Sep 14, 2026
pycytominer equivalence suite Open

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

scverse/mantispy#19 · 1 comment · Opened Sep 14, 2026
Evaluation metrics Open

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

scverse/mantispy#18 · 1 comment · Opened Sep 14, 2026
Feature selection and outlier detection Open

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

scverse/mantispy#16 · Opened Sep 14, 2026
Sphering and batch correction Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/mantispy#17 · Opened Sep 14, 2026
Accessors Open

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

scverse/mantispy#14 · Opened Sep 14, 2026
Normalization Open

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

scverse/mantispy#12 · Opened Sep 14, 2026
Synthetic plate generator with injected artifacts Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/mantispy#9 · Opened Sep 14, 2026
CellProfiler feature-name parser and blocklist Open

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

scverse/mantispy#7 · Opened Sep 14, 2026
Schema, validation and parameter recording Open

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

scverse/mantispy#8 · Opened Sep 14, 2026
Integration Testing CI Test Failure on python 3.14 Open

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

scverse/SnapATAC2#500 · Opened Sep 14, 2026
aggregate(values, by=<labels with no non-background instance>) raises a misleading 'regions do not match' error Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 64/100

scverse/spatialdata#1250 · Opened Sep 13, 2026
aggregate(values, by=<multiscale labels>) crashes with AttributeError despite DataTree being a declared input type Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#1249 · Opened Sep 13, 2026
bounding_box_query(filter_table=True) crashes if the SpatialData object contains an orphan table Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

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

scverse/spatialdata#1248 · Opened Sep 13, 2026
v2.0.0 release on PyPI requires owner change Open

bug

scverse/liana#275 · 2 comments · 2 assignees · Opened Sep 13, 2026
Replace chunks keyword argument in write zarr/h5ad files with more general encoding dict Open

Triage 🩺

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

scverse/anndata#2649 · 1 comment · Opened Sep 11, 2026
Replace chunks keyword argument in write zarr/h5ad files with more general encoding dict Open

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/anndata#2648 · 1 comment · Opened Sep 11, 2026

Showing the newest 100

This page lists what was indexed most recently. Advanced filter has the whole inventory, narrowed by language, difficulty and how long a task takes.

Open advanced filter

scverse

Showing the newest 100

Get new issues in your inbox