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### Type of the feature
- [ ] New function in `sqduipy.im`?
- [x] New function in `squidpy.gr`?
- [ ] New function in `squidpy.pl`?
- [ ] Change an existing functionality, such as default behavi…
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Hi Squidpy team,
It is great to see you are developing platform for spatial analysis. I did not see an example of plotting cell in an image with its real segmentation mask. Will it be on squidpy?
…
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in #64 I had a separation of dataset-analysis tutorials and advanced Squidpy tutorials (Napari, reading spatial data, image container). Could copy this new version to squidpy to have this separation i…
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Could you add Moran's I calculation to Scanpy? It could be used in scIB and to also find variable genes across embedding (could be an alternative to SEMITONES that takes a while to be computed).
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### Type of the feature
- [ ] New function in `sqduipy.im`?
- [ ] New function in `squidpy.gr`?
- [ ] New function in `squidpy.pl`?
- [x] Change an existing functionality, such as default behavi…
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## Description
Came across this error when trying to save the output of the Visium H&E tutorial to disk. Possibly this is an AnnData issue but the problem seems to be the ligand-receptor results …
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### Type of the feature
- [ ] New function in `sqduipy.im`?
- [ ] New function in `squidpy.gr`?
- [ ] New function in `squidpy.pl`?
- [ ] Change an existing functionality, such as default behavi…
giovp updated
3 years ago
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Good day,
I have been trying to follow the vignette Cell-type deconvolution using Tangram but have problems with the deconvolution step. As stated in https://github.com/theislab/squidpy_notebooks/i…
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- [ ] Additional function parameters / changed functionality / changed defaults?
- [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?
- [ ] New plotti…
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...
```python
model = cr.ul.models.GAM(adata)
cr.pl.gene_trends(
adata,
model,
test_sig[0:20],
ncols=3,
data_key="Ms",
color='pterotyping_donor__anno',
time…