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Just fixed https://github.com/scverse/spatialdata-plot/pull/334 and noticed that the extent calculation does not account for the radius of points. In the first version of this picture we calculated th…
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### Analysis Environment
- [x] Installation of `scverse` tools
- [ ] #19
### Analysis Steps
- **Preprocessing**
- [ ] #9
- [ ] #14
- [x] #4
- **Cell typing**
- [ ] #16
- [ ] #3
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You are right, the check on `c_coords` should be one the output data. I merged already because I need to merge #594, which was opened against the current PR. Please can you make a patch for fixing tha…
giovp updated
2 months ago
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Hi @martinkim0 and all
Similarly to https://github.com/scverse/scvi-tools/pull/2249 by @lauradmartens would be great to have a MultiVI version with Poisson or even NB likelihood for ATAC data. How …
vitkl updated
1 month ago
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## Description
When loading CosMx data from FOVs are skipped because they "do not exist in CellComposite folder" or "do not exist in CellLabels folder", however the FOVs do exist in these folders..…
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My system: Ubuntu 23.10
Anndata version: '0.10.5.post1'
When dealing with anndata.var.index the function make_index_unique in utils, was constantly throwing a pandas related error:
`pandas.erro…
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**Is your feature request related to a problem? Please describe.**
Most linear models support passing designs as design matrices and contrasts as contrast vectors. This is the "smallest common denomi…
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### Report
using `uv` for the readthedocs build seems to cause an error with rust, about 'cargo' not found.
The pip install works, while being slower.
Find out what the upstream cause is for that…
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This is a totally random list of things that are currently not best practice in this repository that we eventually want to resolve with #27 by fixing #17 .
1. The package has too many dependencies…