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Seems a regression introduced in #94.
Spaceranger version: 2.1.0
Affects both manual and Cytassist Workflows.
Command executed:
```python
sdata = spatialdata_io.visium("/path/to/spaceranger/…
grst updated
8 months ago
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of scanpy.
- [x] (op…
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Hi,
I'm trying to run the squidpy integration with spatialdata but can't do any spatial calculations (i.e. neighborhood connectivities) because the sdata.table.obsm['spatial'] object is populated w…
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Hi,
I would be grateful for some guidance on the best approach for an analysis. I have also opened a query on the scverse discourse if its easier to move the discussion there: https://discourse.scv…
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Hi,
We use Seurat v3.2.2 and got this warning.
What's wrong with this?
> CT
bun12 updated
7 months ago
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Hi,
This is more a discussion than an issue. Please let me know if we should move that somewhere else.
Let me start with a question: Do you have some mechanism to _select_ a couple of rows in an…
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Hello,
We have a close to final version of scbasset in scvi-tools. I was wondering if the team here was interested in helping benchmark the reproducibility and/or helping with some of the todos on …
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This issue has a quick fix, but I am focusing on something else atm.
The following error is raised by `_io/format.py` on a table that passed validation. The table should have failed the validation.…
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Hi,
Thanks for the tool.
I attempted to cluster 45,000 cells using Leiden algorithm, using default argument `method = "matrix"`. However, I encountered a "memory issue". But. when I changed `me…
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Hello world!
I've read in many papers that when performing a re-clustering of some populations, like T cells or B cells, prior to the step of integration and so on, they re-calculate the HVGs but exc…