anndata
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Annotated data.
I'm reopening https://github.com/theislab/anndata/issues/558 as I'm still having this problem with latest anndata and h5py. It seems that anndata needs to be a bit more defensive about dtypes when writing to...
Example: ```python import anndata as ad, pandas as pd, numpy as np adata = ad.AnnData(np.ones((3, 3)), obs=pd.DataFrame({"a": ["a", 2, 3]})) adata.write_h5ad("tmp.h5ad") ``` The traceback for this ends with: ```pytb TypeError:...
Projects to mention: ## R * [zelkconverter](https://theislab.github.io/zellkonverter/) * [MuData bioconductor package](https://github.com/ilia-kats/MuData) * [AnnData in R](https://cran.r-project.org/web/packages/anndata/readme/README.html) * [MuDataSeurat](https://pmbio.github.io/MuDataSeurat/) ## Julia * [Muon.jl](https://docs.juliahub.com/Muon/QfqCh/0.1.1/)
**Description** When an anndata object is deleted in the current scope the underlying memory is not (reliably) freed as it is for numpy and others. The memory is kept allocated...
We should have a contributing guide here. Really it should be almost exactly the same as scanpy's. Maybe we should just link to that for now?
# AnnData selectors *Note: I will be updating this to be easier to read, just wanted it up to share* ## Use case: Modified IO I would like to able...
When adding large numbers to X I get adata with inf value: ``` y=np.array(2.07547187e+114).reshape(1,1) y Out[72]: array([[2.07547187e+114]]) sc.AnnData(y) Out[73]: AnnData object with n_obs × n_vars = 1 × 1 sc.AnnData(y).X...
The HDF5 file object is not explicitly closed here. In some cases, it causes the file to be locked even after `adata.file.close()`. It can be fixed by using the context...
When `isbacked == True and is_view == True` and the destination file is the same file, anndata will skip writing the `X` and cause unexpected behaviors. ## Code to reproduce:...
Hi I am a relatively new user to the `anndata` package and I think it is awesome. However, when trying to write an `h5ad` file from my object i receive...
