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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

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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
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
`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
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
unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster Open

bug 🚨 element: images 🌌 element: labels 🏷️ needs: triage

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1239 · Opened Sep 11, 2026
spatialdata.models.force_2d() silently drops interior rings (holes) of polygons Open

bug 🚨 element: shapes ▲ models needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1234 · Opened Sep 11, 2026
aggregate(image, by=labels) crashes when the labels have no background (no zero pixels) Open

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

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1230 · Opened Sep 11, 2026
TableModel rejects int8/uint8 instance-key columns although the error message promises 'uint equivalents' (breaks aggregate/to_circles on uint8 labels) Open

bug 🚨 element: labels 🏷️ element: table 📑 models needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1229 · Opened Sep 11, 2026
Substring matching of element names against a single-region table (`element_name in regions` with `regions: str`) Open

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

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1228 · Opened Sep 11, 2026
Case-insensitive element-name uniqueness check only works when the existing name is lowercase Open

API bug 🚨 I/O 💿 needs: triage priority: medium

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

scverse/spatialdata#1221 · Opened Sep 11, 2026
relabel_sequential() fails for every unsigned dtype: OverflowError: Python integer -1 out of bounds for uint16 Open

bug 🚨 element: labels 🏷️ needs: triage priority: high

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1215 · Opened Sep 11, 2026
_filter_labels_element rebuilds set(ids_to_keep) inside a comprehension: O(n_labels × n_keep) in right/inner joins with filter_label_pixels=True Open

bug 🚨 element: labels 🏷️ method: query needs: triage performance 🚀 priority: high

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1208 · Opened Sep 11, 2026
render_labels raises IndexError when the table has rows for instances absent from the mask Open

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

scverse/spatialdata-plot#775 · Opened Sep 4, 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
usage_python vignette fails with mudata >= 0.4 Open

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

scverse/anndataR#511 · Opened Aug 31, 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
solo: --soloBarcodeMate does not require clipping the barcode off the mate, so the barcode bases stay in the aligned read Open

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

scverse/rustar-aligner#227 · Opened Aug 11, 2026
`anndata-hdf5` no longer builds from a clean checkout: `Invalid H5_VERSION: "2.2.0"` Open

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

scverse/anndata-rs#38 · 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
Set bash -euo pipefail as default shell options in all github actions workflows Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/cookiecutter-scverse#549 · 1 comment · Opened Aug 4, 2026
skip `no-commit-to-branch` hook in CI Open

Difficulty 1/5 Under an hour Newbie friendliness 88/100

scverse/cookiecutter-scverse#548 · Opened Aug 4, 2026
Invalid "selection" values in "read_zarr()" should raise an error Open

needs: triage priority: low

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1172 · 2 comments · Opened Aug 3, 2026
CI: `test_info_gene` is flaky — exact-match assertion over best-effort UniProt/NCBI enrichment Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/gget#267 · 1 comment · Opened Jul 12, 2026
CI: `test_cellxgene_adata` fails — cellxgene-census AnnData now exposes a `layers` entry (live-data drift) Open

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

scverse/gget#265 · Opened Jul 8, 2026
Add lazy hdf5anndata to benchmarks Open

triage

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

scverse/anndataR#474 · Opened Jun 23, 2026
Document `numba` sparse plugin types Open

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

scverse/fast-array-utils#165 · Opened Apr 9, 2026
join_spatialelement_table crashes when obs index name matches an existing column Open

needs: triage priority: medium

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

scverse/spatialdata#1099 · 2 comments · Opened Mar 25, 2026
Clarify default hdf5 compression python-interop Open

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

scverse/anndata-rs#20 · 3 comments · Opened Feb 13, 2026
Dask 2026.1.2 breaks ome-zarr-py support Open

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

scverse/spatialdata#1059 · 3 comments · Opened Jan 31, 2026
Scale transform changes aggregate results Open

needs: triage priority: low

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

scverse/spatialdata#1028 · 2 comments · Opened Dec 11, 2025
Incorrect dataset link for `Analyze Xenium data` tutorial Open

Difficulty 1/5 Under an hour Newbie friendliness 68/100

scverse/squidpy#1049 · 4 comments · Opened Oct 23, 2025
Default legend when scaling dotplots Open

Area - Plotting 🌺

Difficulty 2/5 1-3 hours Newbie friendliness 66/100

scverse/scanpy#3576 · 1 comment · 2 reactions · Opened Apr 11, 2025
Test for shapes Open

good first issue

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

scverse/napari-spatialdata#322 · 1 comment · Opened Oct 1, 2024
Stereoseq expected directory structure Open

documentation

Difficulty 2/5 Half a day Newbie friendliness 65/100

scverse/spatialdata-io#161 · 13 comments · Opened Jun 18, 2024
`pl.rank_genes_groups_violin` should be able to pass `**kwds` to `pl.violin` Open

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

scverse/scanpy#2954 · Opened Mar 25, 2024
Community tutorial page Open

documentation

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

scverse/scirpy#495 · Opened Feb 28, 2024
`chunks` needs to be passed to `to_multiscale` otherwise it's ignored Open

needs: triage priority: low

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

scverse/spatialdata#421 · 1 comment · Opened Jan 7, 2024
ome-zarr-py labels logging still appears Open

needs: triage priority: low

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#400 · 3 comments · Opened Nov 13, 2023
Test aggregation when shapes touch but not overlap Open

method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#301 · 1 comment · Opened Jun 19, 2023
`value_key` is ignored in `aggregate()` for images Open

method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#274 · 1 comment · Opened May 22, 2023
Filtering by coordinate system that doesn't exist returns an empty SpatialData object Open

needs: triage priority: low

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

scverse/spatialdata#239 · 3 comments · Opened May 4, 2023
Fix typo in argument names in `align_elements_using_landmarks()` Open

needs: triage priority: low

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

scverse/spatialdata#229 · 1 comment · Opened Apr 18, 2023

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