anndata
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Annotated data.
I would support JAX as another backend. Would probably be worth opening another issue for tracking JAX as a backend. For IO, I was thinking that could be done with...
We would like to expose an API for working with completley backed `AnnData` (and `MuData`) objects. # Current state Currently we only expose limited functionality for this, `backed` mode, `AnnLoader`...
This is an implementation proposal draft for unifying `.X` and layers as mentioned e.g. in #244. Expanding on previous issues, this one tracks concrete implementation details for achieving the end...
Tests in test_backed_sparse.py, test_hdf5_backing.py, test_inplace_subset.py, test_views.py fail with pandas 1.4
Originally noticed this with errors in **{zellkonverter}** (see https://github.com/theislab/zellkonverter/issues/59) but can confirm it happens with straight Python. ```python import anndata import numpy as np X = np.random.random((100, 1000)) adata =...
This is a draft to address #675. As with [mudata](https://github.com/scverse/mudata), it is collapsable — [check out e.g. this notebook](https://mudata.readthedocs.io/en/latest/notebooks/quickstart_mudata.html) with `mudata`. Maybe we can iterate on an implementation of it,...
Allow AnnData objects have `.X` as a `DeviceArray`. Layer support should also be there but seems to currently fail just as it does e.g. for `DaskArray`, as mentioned in #693....
As mentioned in #693, the current writer fails if a `DaskArray` is a layer but doesn't fail when it's just an `.X`: ```py import numpy as np d = np.random.normal(size=1000).reshape(100,...
It would be nice if we could seamlessly hold `dask` arrays and dataframes inside of an AnnData object. I would consider this issue closed once most operations on an AnnData...
[Cellarity](https://cellarity.com/) benefits from anndata / scanpy open-source development and is proud to contribute a class I wrote in July 2020 to speed up our Platform. GroupBy class supports grouping and...
