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Vince - here:
```{python, message=FALSE}
import scanpy as sc
pp3k = sc.datasets.pbmc3k()
pp3k
...
I have a python environment called singleCell which has the right packages, but how do I m…
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https://github.com/scverse/squidpy/blob/16a9885976e24778664c81c05a9b592b2bd4a237/src/squidpy/_docs.py#L222-L223
The documentation for `legend_loc` in `spatial_scatter` refers to `matplotlib.legend.…
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I meet the 'scanpy.api' error when I run SAVERX on my own samples
[1] "Input is a data matrix"
[1] "Use a pretrained model: Yes"
[1] "Data species is: Human"
[1] "Pretrained weights file is: …
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I used to use scanpy python package for down-stream analysis.
I wonder how the predicted gene expressions can be analyzed in Anndata (Scanpy).
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Thank you for your cool package. I've been experimenting with it on my own data lately.
The issue that arose after installing it (from PyPI) is that the 'scanpy==1.4.6' dependency is quite outdated…
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scanpy is a popular python package for scRNA-seq analysis and processing.
It would be great to accept anndata objects.
https://icb-scanpy.readthedocs-hosted.com/en/stable/
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### Description of the bug
I wish I could state anything that would sound helpful here. The script triggering the issue is ./modules/local/celda/decontx/templates/decontx.py and I agree that sizes…
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Once all relevant tutorials are integrated on `scverse.org/learn`, probably the scanpy tutorials page should be retired altogether and just link there.
All other scverse core package should at lea…
grst updated
5 months ago
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"scanpy-scripts" is currently having dependency problems. This:
`johnnydep --output-format pinned scanpy-scripts
`
fails in a manner which might not be what you intended. In any case, it did…
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Successfully installed SAMap, but when I try to run
>>> from samap.mapping import SAMAP
I get the following error related scanpy import:
ImportError: cannot import name 'get_cmap' from 'matplotl…