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## Description
Nanostring CosMx datasets have a new file export format through TileDB, https://nanostring.com/wp-content/uploads/2023/01/LiverPublicDataRelease.html
They no longer give .csv file…
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Hi,
I am trying to import a dataset from 10X Visium H&E
I am importing the dataset with:
```python
adata = sq.read.visium('path')
adata.var_names_make_unique()
```
Then pre-processing:
```py…
Lem-P updated
2 weeks ago
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### Is this a new feature, an improvement, or a change to existing functionality?
New Feature
### How would you describe the priority of this feature request
Low (would be nice)
### Please…
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Hello
I tried to pip install the package in spyder. But it failed, below is lines from console. tried .whl or the .gz, both failed.
pip install scTriangulate
Collecting scTriangulate
Using c…
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Currently, squidpy focusses mostly on local [spatial neighborhoods ](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_vizgen_mouse_liver.html#neighborhood-enrichment) for niche an…
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Hi! Thanks for writing Squidpy! Its really amazing!
I'm running into an issue and I'm not sure if its an issue with squidpy itself or how I'm running the code or space on my computer. I cannot ru…
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Hi,
where can I find omnipath tutorials? I have installed omnipath(Python client for the OmniPath web service), but I don't know how to use it and I cannot find documentation on this github. Or, who …
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There may be fields in the underlying data that would be helpful to data downloaders but overwhelm Explorer's visualization capabilities. We'd like to hear form the community if this functionality wou…
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I think it makes sense to deprecate and then remove `sc.read_visium`. and `sc.pl.spatial` since I don't plan to maintain it here anymore and updated versions are present in Squidpy. What do you think …
giovp updated
7 months ago
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## Description
WARNING: Failed to open the url with default certificates, trying with certifi.
Visium_FFPE_Mouse_Brain. Error: HTTP Error 403: Forbidden
WARNING: Failed to open the url with def…