Issues

• [question] How to concat "large-scale" data (>5M cells)

  question
  scverse/anndata#2677 · Filter by author JuanTejedor opened on Oct 1, 2026
  2

  

• A.uns accessors

  topic: api
  Enhancement

  scverse/anndata#2657 · Filter by author flying-sheep opened on Sep 22, 2026

• Replace chunks keyword argument in write zarr/h5ad files with more general encoding dict

  Enhancement

  scverse/anndata#2648 · Filter by author joshua-gould opened on Sep 11, 2026
  1

• Side effect when writing string columns to zarr

  question
  scverse/anndata#2610 · Filter by author ajkswamy opened on Aug 19, 2026
  1

• Disable zarr auto sharding with dask as it's much slower

  Bug

  scverse/anndata#2598 · Filter by author joshua-gould opened on Aug 10, 2026
  2

• No partial read for nullable-string-array

  topic: io
  Enhancement

  scverse/anndata#2595 · Filter by author Koncopd opened on Aug 7, 2026
  7

• read_zarr fails with obs columns that differ only by case

  backend: zarrtopic: ioupstream
  Bug

  scverse/anndata#2576 · Filter by author cvduffy opened on Jul 28, 2026
  2

• Migrate to cs{r,c}_array internally/externally

  type: sparse 🫥
  Enhancement

  scverse/anndata#2477 · Filter by author ilan-gold opened on Jun 3, 2026 · 0.14.0
  3

• pandas>=3 breaks with xarray.Dataset in obsm/varm when using anndata.concat and load_annotation_index

  Bug

  scverse/anndata#2475 · Filter by author ilan-gold opened on Jun 2, 2026

• make ref path available in write_dispatched and read_dispatched callback

  topic: apitopic: io
  Enhancement

  scverse/anndata#2457 · Filter by author flying-sheep opened on May 19, 2026

• Allow any unicode incl. / and \ in obsm keys, obs columns, uns keys, …

  topic: io
  Enhancement

  scverse/anndata#2450 · Filter by author flying-sheep opened on May 18, 2026 · 0.14.0
  3

• write_zarr fails with LocalCUDACluster (dask-cuda) when adata.X has been persisted

  Bug

  scverse/anndata#2444 · Filter by author Intron7 opened on May 13, 2026
  2

• layers can be 3D on-disk

  topic: io
  Bug

  scverse/anndata#2430 · Filter by author ilan-gold opened on May 8, 2026 · 0.14.0
  4

• make write_zarr respect the public chunks parameter when the input is sparse

  Enhancement

  scverse/anndata#2415 · Filter by author mkarikom opened on May 2, 2026
  4

• Support pairwise for concat_on_disk

  Enhancement

  scverse/anndata#2414 · Filter by author alam-shahul opened on Apr 30, 2026

• Expose canonical section-name tuple alongside iter_outer

  scverse/anndata#2401 · Filter by author katosh opened on Apr 21, 2026

• concat_on_disk with join='outer' doesn't retain all .obsm fields

  Bug

  scverse/anndata#2394 · Filter by author alam-shahul opened on Apr 16, 2026 · 0.14.0
  2

• Support sparse pandas DataFrames

  type: dataframe 🧮type: sparse 🫥
  Enhancement

  scverse/anndata#2380 · Filter by author WeilerP opened on Apr 2, 2026
  13

• obs i.e., axis=0 column joining + anndata.concat is underspecified

  good first issuetopic: apitype: dataframe 🧮
  Enhancement

  scverse/anndata#2374 · Filter by author ilan-gold opened on Mar 23, 2026
  5

• Lenient write

  topic: io
  Enhancement

  scverse/anndata#2373 · Filter by author flying-sheep opened on Mar 22, 2026

• Error writing recarray with all nan values

  stale
  Bug

  scverse/anndata#2363 · Filter by author lazappi opened on Mar 11, 2026
  9

• Setting pandas.DataFrame with ArrayView produces all NaN

  staletopic: views 👀
  Bug

  scverse/anndata#2348 · Filter by author ilan-gold opened on Feb 13, 2026
  3

• Make all warnings into errors

  testing
  scverse/anndata#2343 · Filter by author flying-sheep opened on Feb 12, 2026

• Unable to rechunk a view of a 2-d sliced AnnData with a dask array

  Bug

  scverse/anndata#2330 · Filter by author joshua-gould opened on Feb 5, 2026
  8

• Why is there a need to wrap dask array views in DaskArrayView

  question
  scverse/anndata#2329 · Filter by author joshua-gould opened on Feb 4, 2026
  5