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### Problem
I'm running cell2location on an HPC cluster to enable use of a GPU. Cell2location runs fine (Thanks for the great package!) and I'm able to make plots interactively in Jupyter after…
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Hi,
I have created an anndataobject manually from an seuratobject, and it works for all of my python downstream analysis.
![image](https://github.com/user-attachments/assets/d50ab8b9-e42b-4377-b32…
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Hello,
Thank you for developing so nice software!
Thank you in advance for great help!
Best,
Yue
```
> cellchat cellchat cellchat cellchat cellchat cellchat netVisual_embedding(c…
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Hi
I was wondering if there is any way to use/explore spatial data in cell browser? Something similar to Loupe browser if possible
Thanks
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## Describe the bug
rule create_qc_sheet:
input: projects/visium_demo/processed_data/Mouse_Brain_Rep1/illumina/complete_data/star.Log.final.out, projects/visium_demo/processed_data/Mouse_Brain_R…
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Hi,
I processed my single cell data using scanpy's preprocessing script. I have two samples - control and mutant that i merged before processing it. When I ran it through the cardec pipeline, i'm g…
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Hey!
I have recently gotten a quite deeply clinically phenotyped dataset and have been pondering how the metadata should best be stored in an anndata object. It feels redundant to duplicate a label…
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Hello, Based on your latest code, data and provided parameters, I tested the results in the paper again using the environment you provided and found that the results are still **very bad**
**For the …
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I am trying to do singlecellVR starting from a seurat object. I have tried with my own data and the pbmc example dataset shown. I can convert to .loom just fine. I get a KeyError: 'umap_cell_embeddi…
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Hi there,
When storing a matrix with row names and column names in the `uns` slot, these are removed. I assume that is to align with the python `numpy` implementation where these are not supported.…