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Allow non-transposed H5ADMatrix #67

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Allow non-transposed H5ADMatrix#67

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@lazappi
lazappi
opened on Nov 20, 2025

We are planning to add DelayedArray support to {anndataR} and one option that would make sense is to use the H5ADMatrix class (see scverse/anndataR#128). However, the object is currently transposed to match R conventions while AnnData uses Python conventions. Would it be possible to allow a non-transposed H5ADMatrix (probably with a transpose argument somewhere)?

Alternatively, do you have an idea how much overhead there is to doing t(h5ad_matrix) which returns a regular DelayedMatrix? If that's not costly maybe it's a simpler option.

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