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### Description
I have a few questions about the `interaction_matrix` function. First, am I using the same definition as you?
To me, interaction matrix `M` for graph `G` and labelling `c`, `M[i,…
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Hi,
I got **Visium** data. I read it with scanpy and save it to h5ad format with anndata.write()
When I attempted to load the file to sepal, I got an error for not having the field 'name' (KeyError:…
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I'm trying to run `sq.gr.co_occurrence(adata, cluster_key="cluster")` on the 4i dataset (~270k obs so adj mat quite large) and the process is...simply killed
```bash
>>> sq.gr.co_occurrence(adata,…
giovp updated
3 years ago
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@hspitzer I came up with a few points regarding the `ImageContainer`. Let me know what you think:
1. `squidpy.im.segment_crops` is unused (not expored in `squidpy.im`), as well as `evaluate_nuclei_…
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I'm trying to commit some tutorials to a branch. During this process I noticed some issues with the pre-commit hook and tox.
I have installed the pre-commit hook using `pre-commit install` in `squidp…
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Create datasets module with the datasets listed in https://github.com/theislab/squidpy_notebooks/issues/8
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Hi,
was wondering: is there any plan to provide an API to use cellphonedb from within python? This would make it super convenient to include cellphonedb in a standard single cell analysis workflow (e…
giovp updated
3 years ago
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in #172 @michalk8 removed `squidpy.utils.py`. Did the functions go somewhere else? I was using the read function to read in adata + image container.
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Tried to find this function but I am not sure if it got renamed or removed. May I please be pointed to it to update notebooks/examples? Thanks.
![image](https://user-images.githubusercontent.com/2761…
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