scverse/anndata

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Stars: 773
Forks: 209
Open beginner issues: 0
Indexed issues: 187
Avg merge: 19h 41m
Merged PRs (30d): 32

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

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187 open issues indexed

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
write_zarr with dask array should use dask chunks by default Open

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

scverse/anndata#2627 · 6 comments · Opened Sep 1, 2026
Side effect when writing string columns to zarr Open

question

Difficulty 3/5 1-2 days Newbie friendliness 50/100

scverse/anndata#2610 · 1 comment · 1 reaction · Opened Aug 19, 2026
Disable zarr auto sharding with dask as it's much slower Open

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

scverse/anndata#2598 · 1 comment · Opened Aug 10, 2026
No partial read for nullable-string-array Open

topic: io

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

scverse/anndata#2595 · 7 comments · Opened Aug 7, 2026
read_zarr fails with obs columns that differ only by case Open

backend: zarr topic: io upstream

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

scverse/anndata#2576 · 2 comments · Opened Jul 28, 2026
Migrate to `cs{r,c}_array` internally/externally Open

type: sparse 🫥

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

scverse/anndata#2477 · 2 comments · 2 reactions · Opened Jun 3, 2026
`pandas>=3` breaks with `xarray.Dataset` in `obsm`/`varm` when using `anndata.concat` and `load_annotation_index` Open

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

scverse/anndata#2475 · Opened Jun 2, 2026
make ref path available in `write_dispatched` and `read_dispatched` callback Open

topic: api topic: io

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

scverse/anndata#2457 · Opened May 19, 2026
Allow any unicode incl. `/` and `\` in `obsm` keys, `obs` columns, `uns` keys, … Open

topic: io

Difficulty 5/5 Over a week Newbie friendliness 28/100

scverse/anndata#2450 · 3 comments · Opened May 18, 2026
write_zarr fails with LocalCUDACluster (dask-cuda) when adata.X has been persisted Open

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

scverse/anndata#2444 · 2 comments · Opened May 13, 2026
`layers` can be 3D on-disk Open

topic: io

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

scverse/anndata#2430 · 4 comments · 1 reaction · Opened May 8, 2026
make write_zarr respect the public chunks parameter when the input is sparse Open

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

scverse/anndata#2415 · 4 comments · Opened May 2, 2026
Support `pairwise` for `concat_on_disk` Open

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

scverse/anndata#2414 · Opened Apr 30, 2026
Expose canonical section-name tuple alongside `iter_outer` Open

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

scverse/anndata#2401 · Opened Apr 21, 2026
`concat_on_disk` with `join='outer'` doesn't retain all `.obsm` fields Open

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

scverse/anndata#2394 · 2 comments · Opened Apr 16, 2026
Support sparse pandas DataFrames Open

type: dataframe 🧮 type: sparse 🫥

Difficulty 3/5 1-2 days Newbie friendliness 52/100

scverse/anndata#2380 · 13 comments · Opened Apr 2, 2026
`obs` i.e., `axis=0` column joining + `anndata.concat` is underspecified Open

good first issue topic: api type: dataframe 🧮

Difficulty 5/5 Over a week Newbie friendliness 32/100

scverse/anndata#2374 · 5 comments · Opened Mar 23, 2026
Lenient write Open

topic: io

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

scverse/anndata#2373 · Opened Mar 22, 2026
Error writing `recarray` with all `nan` values Open

stale

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

scverse/anndata#2363 · 9 comments · Opened Mar 11, 2026
Setting `pandas.DataFrame` with `ArrayView` produces all `NaN` Open

stale topic: views 👀

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/anndata#2348 · 3 comments · Opened Feb 13, 2026
Make all warnings into errors Open

testing

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

scverse/anndata#2343 · Opened Feb 12, 2026
Unable to rechunk a view of a 2-d sliced AnnData with a dask array Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

scverse/anndata#2330 · 8 comments · Opened Feb 5, 2026
Why is there a need to wrap dask array views in DaskArrayView Open

question

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

scverse/anndata#2329 · 5 comments · Opened Feb 4, 2026
Virtual concatenation support for `concat_on_disk` Open

scverse/anndata#2311 · 1 comment · 1 assignee · Opened Jan 22, 2026
feat: Chunking for categorical `categories` string arrays only Open

backend: hdf5 backend: zarr topic: cloud ☁️ topic: io

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

scverse/anndata#2296 · Opened Jan 14, 2026
feat: Efficient category count and partial loading for lazy AnnData Open

backend: hdf5 backend: zarr topic: backed topic: cloud ☁️

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

scverse/anndata#2283 · 14 comments · Opened Jan 6, 2026
`concat_on_disk` Does not respect underlying anndatas chunking & sharding for Zarr Open

backend: zarr

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

scverse/anndata#2281 · 3 comments · Opened Jan 5, 2026
Keep providing a non-nullable string type? Open

topic: io type: dataframe 🧮

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

scverse/anndata#2252 · 7 comments · Opened Dec 16, 2025
AnnData.write_zarr streaming to a tar archive? Open

Needs info❔ question

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

scverse/anndata#2249 · 4 comments · Opened Dec 11, 2025
i/o of different index types Open

topic: indexing topic: io type: dataframe 🧮

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

scverse/anndata#2241 · 1 reaction · Opened Dec 8, 2025
Handle new zarr dtypes (both custom and datetime) Open

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

scverse/anndata#2238 · Opened Dec 3, 2025
anndata.io.write_elem with an AnnData object raises error on chunk_shape when using chunks argument Open

stale

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

scverse/anndata#2193 · 8 comments · Opened Nov 2, 2025
Custom `to_memory` handling `compute` Open

type: dask array

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

scverse/anndata#2185 · 1 comment · Opened Oct 28, 2025
Add type-annotation, enable mypy to check it Open

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

scverse/anndata#2173 · 7 comments · 1 reaction · Opened Oct 25, 2025
Error calling numpy nan functions on views Open

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

scverse/anndata#2149 · 9 comments · Opened Oct 10, 2025
`read_lazy` kwarg for not using dask Open

performance 🐌 topic: backed topic: cloud ☁️ topic: io type: dask array

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

scverse/anndata#2147 · 7 comments · 1 reaction · Opened Oct 9, 2025
Show tqdm progress when loading large datasets Open

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

scverse/anndata#2144 · 2 comments · Opened Oct 3, 2025
Can you change `use_cuda=False` to `device` so we can select `cuda`, `mps`, or `cpu`? Open

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

scverse/anndata#2082 · 5 comments · Opened Aug 20, 2025
Support Apache Arrow data ingest Open

topic: conversion

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

scverse/anndata#2078 · 10 comments · Opened Aug 12, 2025
new uns_merge strategy for ad.concat() Open

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

scverse/anndata#2068 · 7 comments · Opened Jul 31, 2025
`anndata` `0.2.0` on-disk format Open

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

scverse/anndata#2060 · 4 comments · Opened Jul 29, 2025
Compatibility profiles for writing Open

topic: compatibility topic: io

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

scverse/anndata#2057 · 3 comments · Opened Jul 29, 2025
`DataFrame` API for `obs` and `var` keys via runtime-checkable `Protocol` Open

topic: api type: dataframe 🧮

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

scverse/anndata#2043 · 6 comments · 2 reactions · Opened Jul 22, 2025
feat: sensible chunk defaults for dask Open

good first issue performance 🐌 type: dask array

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

scverse/anndata#2036 · 5 comments · Opened Jul 17, 2025
Test failures as of 0.11.4 on NixOS Open

stale

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

scverse/anndata#2017 · 13 comments · Opened Jun 20, 2025
Consolidated Metadata Handling Open

backend: zarr topic: backed topic: cloud ☁️ topic: io

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

scverse/anndata#2016 · Opened Jun 20, 2025
Allow storing heterogeneous lists in .uns (as JSON or so) Open

backend: hdf5 backend: zarr topic: io

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

scverse/anndata#1979 · 7 comments · Opened May 7, 2025
Writing zarr as a zipped directory Open

backend: zarr

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

scverse/anndata#1971 · 5 comments · Opened Apr 15, 2025

scverse/anndata

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