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o See this PR for anndataR (Bioconductor package) by Mark Keller and
Artür Manukyan: https://github.com/scverse/anndataR/pull/190
o In addition to looking at what Rarr has to offer to tackle the tasks
below (array dimnames, groups, sparse arrays), take a look at
pizzarr: https://github.com/keller-mark/pizzarr
o writeZarrArray() needs to write the array dimnames to disk.
o Add support for handling groups (or hierarchies of groups) of Zarr arrays.
o Add support for sparse arrays. Does Zarr have native support for sparse
arrays or do we need to use the same approach as in H5SparseMatrixSeed?
If the latter, then Artür already has a working version of that in
https://github.com/BIMSBbioinfo/ZarrArray
See his comment in the spatialdata-devel channel on Zulip:
https://community-bioc.zulipchat.com/#narrow/channel/507643-spatialdata-devel/topic/anndataR-zarr/near/561372916
o Improve support for Zarr v3. For example, one issue at the moment (Rarr
1.11.24) is that Rarr::create_empty_zarr_array() only supports creation
of Zarr v2 datasets. As a consequence, writeZarrArray(), which is based
on Rarr::create_empty_zarr_array(), can only write in Zarr v2 format at
the moment.
- 2026/04/02 update: writeZarrArray() now has a 'zarr_version' argument
that is set to 3 by default.
o Benchmarking:
- Read/write speed compared with hdf5.
- Impact of chunk geometry on read/write operations.
- Concurrency: is it suported for reading and writing, or only for reading?
(Note that hdf5 is notorious for not supporting concurrent writing to
the same dataset.) Do some benchmarking using BiocParallel.
After ZarrArray is accepted and added to BioC 3.23
==================================================
o Register realization backend _ZarrArray in the DelayedArray package.
o Implement saveZarrSummarizedExperiment() and
loadZarrSummarizedExperiment() for saving/loading
a Zarr-based SummarizedExperiment object to/from disk.