Issues

• Integration Testing CI Test Failure on python 3.14

  scverse/anndataR#565 · Filter by author scverse-issue-creator opened on Oct 31, 2026

• Should X become a layer internally, as in Python anndata >= 0.13?

  design
  scverse/anndataR#562 · Filter by author rcannood opened on Oct 30, 2026

• write_zarr() fails on backed objects

  backedbugzarr
  scverse/anndataR#559 · Filter by author rcannood opened on Oct 28, 2026
  3

• Backed as_Seurat() and as_SingleCellExperiment() fail on csc graphs in obsp

  backedbugSeuratSingleCellExperiment
  scverse/anndataR#558 · Filter by author rcannood opened on Oct 28, 2026

• Consider using S4Vectors::DataFrame instead of data.frame for obs/var

  designtriage
  Enhancement

  scverse/anndataR#554 · Filter by author lazappi opened on Oct 25, 2026
  3

• Logical matrices with NA written to H5AD or Zarr can't be read back

  Bug

  scverse/anndataR#545 · Filter by author ellispatrick opened on Oct 22, 2026

• Should failing to read an element be an error instead of a warning?

  design
  Enhancement

  scverse/anndataR#544 · Filter by author rcannood opened on Oct 22, 2026
  1

• Auto-chunk Zarr writes, as #424 did for HDF5

  Enhancement

  scverse/anndataR#541 · Filter by author ellispatrick opened on Oct 22, 2026
  1

• Renaming obs_names/var_names on a backed object leaves obsm/varm data frame indices stale

  bugtriage
  Bug

  scverse/anndataR#537 · Filter by author rcannood opened on Oct 22, 2026

• Update bencher from token to key

  bugtriage
  Bug

  scverse/anndataR#532 · Filter by author rcannood opened on Oct 21, 2026

• read_h5ad() error when sparse X indices are out of range

  bug
  Bug

  scverse/anndataR#531 · Filter by author igordot opened on Oct 20, 2026
  3

• Ensure HTTPS is enabled

  Task

  scverse/anndataR#524 · Filter by author Zethson opened on Sep 23, 2026

• Test reading/writing H5AD files across multiple anndata releases

  developerh5ad
  Enhancement

  scverse/anndataR#516 · Filter by author rcannood opened on Aug 31, 2026

• Full support for Python anndata >= 0.13

  new feature
  Enhancement

  scverse/anndataR#514 · Filter by author rcannood opened on Aug 31, 2026
  5

• Implement compression for boolean datasets

  h5adnew feature
  Enhancement

  scverse/anndataR#513 · Filter by author rcannood opened on Aug 31, 2026

• usage_python vignette fails with mudata >= 0.4

  Bug

  scverse/anndataR#511 · Filter by author rcannood opened on Aug 31, 2026
  1

• Spec deviation for Zarr scalar strings

  bugtriage
  Bug

  scverse/anndataR#500 · Filter by author Bisaloo opened on Aug 12, 2026
  2

• Seurat object CITE-seq data conversion do AnnData, scanpy read issue

  questiontriage
  scverse/anndataR#494 · Filter by author Lodevdv opened on Jul 29, 2026
  3

• hdf5_adata$as_Seurat fails when features contain _

  bugtriage
  Bug

  scverse/anndataR#476 · Filter by author doliv071 opened on Jul 9, 2026
  3

• Add lazy hdf5anndata to benchmarks

  triage
  Enhancement

  scverse/anndataR#474 · Filter by author rcannood opened on Jun 23, 2026

• Allow reading/writing from a path in a HDF5 file

  h5adtriage
  Enhancement

  scverse/anndataR#466 · Filter by author lazappi opened on Jun 11, 2026
  

• Consolidated Zarr metadata at the root of the anndata zarr store

  zarr
  Enhancement

  scverse/anndataR#461 · Filter by author Bisaloo opened on May 25, 2026
  1

• Add optional data.frame conversion for Matrix column names (Seurat Conversion)

  triage
  scverse/anndataR#459 · Filter by author samuel-marsh opened on May 21, 2026

• Extract shared encoding helpers from H5AD and Zarr backends

  h5adzarr
  Task

  scverse/anndataR#445 · Filter by author lazappi opened on Apr 15, 2026

• Investigate how missing values are handled in string arrays

  h5adzarr
  Task

  scverse/anndataR#444 · Filter by author lazappi opened on Apr 15, 2026