anndata
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scverse
Annotated data.
``` import anndata import numpy as np import pandas as pd adata = anndata.AnnData( X=np.array([[-1.0, 0, 2.0, 10], [3, 5, 0, 1], [0, 0, 0, 0]]), var=pd.DataFrame(index=['A', 'B', 'C', 'E']),...
Hi all! I'm currently reviewing anndata's submission to JOSS (openjournals/joss-reviews#4371). I think the paper is very well written and is worthy of publication at JOSS. However, in going over the...
Integrate the benchmark suite started in https://github.com/ivirshup/anndata-benchmarks into this package. ## Initial Goals - [ ] Benchmarks for all basic operations - [ ] Documentation on how to run and...
In reference to #263 I am facing a similar issue now. I am concatenating two identical anndatas (as a test). They have the same var dataframe under `adata.raw.var` and `adata2.raw.var`....
I am trying to output a table from h5ad file. These are codes. import numpy as np import pandas as pd import anndata as ad from scipy.sparse import csr_matrix adata...
I'm opening this issue to track and discuss how our data structure differs from xarray. Ideally I would close it when AnnData could easily be implemented via xarray. *Some previous...
there were no problem reading .h5ad file but all of the sudden, this error came up and unable to read .h5ad files,, someone have any idea?? Thank you!!
We should have a simple comparative benchmark (with prose) comparing using AnnData and our on disk format to alternative structures. Initial measurements could look at: * IO time * IO...
We transitioned from editing the paper in https://github.com/ivirshup/anndata-paper to editing it in this PR, as required for submitting to https://joss.theoj.org/. This branch does not need to be merged into the...
