anndata

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I got this error when running `read_zarr` ``` --------------------------------------------------------------------------- NameError Traceback (most recent call last) /tmp/ipykernel_14805/1560565781.py in ----> 1 iss=anndata.read_zarr("https://b.cog.sanger.ac.uk/datasets/ISS/0.0.1/anndata.zarr") ~/miniconda3/envs/flng/lib/python3.8/site-packages/anndata/_io/read.py in read_zarr(*_, **__) 24 25 def read_zarr(*_, **__): --->...

brianpenghe

Writing r+ backed adata causes error in raw

4

I read and write r+ backed adata (containing raw) as follows: ``` adata=sc.read_h5ad(path,backed='r+') # Add some data to obs # ... adata.write(path) ``` I get the following error due to...

Hrovatin

Formalize support for buffer IO for .h5ad

1

So far we only support reading/writing from paths, this PR adds tests / type hints for binary buffers / file-like objects. - [x] TODO: tests

flying-sheep

first attempt to support awkward arrays

43

First draft at supporting [awkward arrays](https://awkward-array.org/quickstart.html#). As discussed with @ivirshup this would be useful for Squidpy @hspitzer (discussed also here #609 ) and potentially @Zethson EHR project. Here's a walkthrough...

giovp

[DOCS] typo in varp docstring

1

alexlenail

Anndata.concat([adata1, adata2, ...]) not working as expected

1

Hi I am trying to concatenate multiple anndata objects into one. If I consider axis=0, it is combining along .obs and if I consider axis=1, it is combining along .var....

mahati-acog

Issues subsetting AnnData object with reticulate

3

Hi, I'm using reticulate to perform the scanpy tutorial for single cell data analysis. #R library(reticulate) reticulate::repl_python() #mkdir data #wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz #cd data; tar -xzf pbmc3k_filtered_gene_bc_matrices.tar.gz #python import...

imerelli

Older versions of anndata throw unintuitive errors when trying to read newer formats

8

Hi, I wanted to get help on an error reading h5ads created by the `0.8.0rc` version of anndata. In my experience, h5ads that are created using `0.8.0rc1` cannot be opened...

mukundctx

I get a write error:

3

I get a write error: `Above error raised while writing key 0 of from /.` if a name of the index to the var table is an int. Setting the...

zznx

Integration with Loompy

1

@edg1983 mentioned [here](https://github.com/theislab/scvelo/issues/864) that anndata fails to read in the loom files generated by loompy (necessary to link loompy and scvelo). I've fixed this locally by changing some code in...

pranzatelli