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Dear Developer,
It's a great package, while I am new to this. I have a silly question about the IMC data analysis. What's the exact data input of this # load the pre-processed dataset adata = sq.…
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Hi all,
I was wondering whether it could be possible to retrieve the matplotlib figure instance created within a nhood enrichment test, or - even better - pass a matplotlib axes object to `sq.gr.nh…
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Hello,
Thank you for developing this nice tool! I've been using it to run some neighborhood enrichment analysis, and I noticed that the enrichment z score between pairs of the same cluster types …
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Hey @cgohlke :wave:
With the recent 2202.04.22, it seems like the breaking changes to `is_shaped` / `shaped_metadata` / `shaped_description` are _really_ breaking. Our CI picked it up: https://git…
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We want to have preview galleries like Squidpy which link to respective notebooks. Ideally they would also have a binder link or directly open Binder to run these notebooks.
![Uploading image.png…]…
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Hi,
how to show x and y coordinates on scanpy and squidpy plot ?
Now, the sc.pl.umap() and sc.pl.spatial() don't show axes coordinates by default.
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**Describe the bug**
When using pathml with [virtualenv](https://virtualenv.pypa.io/en/latest/) instead of conda, there is an issue where openslide can not be correctly used straight out of the box. …
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Hi,
the scaled data is in adata.X, can I use this with sq.gr.spatial_autocorr(adata, mode="moran") ?
And, when I used sq.gr.spatial_autocorr(adata, use_raw=True, mode="moran"), an error occurred:
…
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Hello,
I am loading a 10x visium experiment and would like to use the squidpy interactive viewer. However, I am running into an issue with img.interactive(). KeyError: "Unable to get the spot d…
dst53 updated
2 years ago
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### Version
22.10
### Which installation method(s) does this occur on?
Conda
### Describe the bug.
When i create a graph with `from_cudf_adjlist` it is not weighted. The resulting graph also do…