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Dear Author,
Firstly, I would like to express my appreciation for your excellent work on Sagenet. It's a fantastic tool that has been very helpful. However, I've encountered a couple of issues whil…
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Hi,
When I run sq.gr.nhood_enrichment(sdata["table"], n_jobs=10, cluster_key='id'), the following error occurred:
https://github.com/scverse/squidpy/issues/867
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Continuation of a cofest project, and putting here for discussion.
Problem:
- Several large tools use entire directories of data as their inputs that require properly structured directories that o…
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This would be immensely useful for the GPU data science community as it would start to enable pipelines fully on GPU.
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### Report
Hi developers,
I'm trying to run `cellcharter` on my own `Stereo-Seq` spatial transcriptomics data. I have seven samples and tried to run `cellcharter` following the [Spatial clustering o…
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Dear @willtownes,
Thanks for making the code for Nonnegative Spatial Factorization available! I really want to start playing with this. Would it be possible for you to create a Jupyter/Colab Notebo…
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Hi, I found an error from the tutorial:
![image](https://github.com/broadinstitute/Tangram/assets/43333475/57b2cdba-ba61-4cb4-b27c-fc7b79a0c795)
Moreover, the final output with deconvolution res…
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Hi, I tried to impute my own spatial datasets (as mouse) with the tutorial for imputation. However, it seems that I cannot impute it with a bug:
```
ValueError: None of AnnData.var.index found in …
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**User story**
```[tasklist]
### Tasks
- [x] Shapes - circles (with fixed radius)
- [ ] Shapes - circles with radius column
- [ ] [Shapes - polygons](https://github.com/vitessce/vitessce/issues…
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while trying to access `grid_layout` with
`viewer.window.qt_viewer.controls.widgets[viewer.layers["CD36:X:image1"]].grid_layout`
I get:
```
/var/folders/3t/lc9m5zv966934dq4d6gf6l60g_dj6h/T/ipy…
giovp updated
2 years ago