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@bgruening @Delphine-L I was pointed to this tutorial recently https://training.galaxyproject.org/training-material/topics/galaxy-interface/tutorials/galaxy-intro-jupyter/tutorial.html which suggests …
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## Description
Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9
## Minimal reproducible example
```python
adata = sq.read.vizgen(
…
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### Description of feature
We are currently using custom code as a work-around as a replacement for the `to_legacy_anndata` function from `spatialdata_io`, which did not exist when the work with Spat…
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Hi
## Description
We have used Space Ranger 2.1.0 to generate spatial RNA-sequencing data for some samples. When reading the Space Ranger output using the `sq.read.visium()` function, it seems i…
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I am re-opening this issue because I am still having problems running squidpy.gr.co_occurrence() with n_splits>1. I noticed that this has been previously discussed [here](https://github.com/scverse/sq…
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Hello,
I have a question about the deconvolution process. As I understand it, there are 2 steps: (1) segmentation by watershed algorithms that gives the cell_count and (2) deconvolution by alignment…
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https://github.com/theislab/scanpy/blob/8736fc3b02a6af3b7214481c2cf78a3f8f5e06bd/scanpy/tests/test_read_10x.py#L105
giovp updated
2 years ago
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**Describe the bug**
When loading a spatial AnnData file, only embeddings like "pca", "umap" are offered but not "spatial". According to the [documentation](https://github.com/chanzuckerberg/cellxg…
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Hello, I posted a question previously in Seurat (https://github.com/satijalab/seurat/issues/9036) but they don't have bandwidth to implement this feature. Since squidpy has a similar function (https:/…
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## Description
I installed suidpy in a virtual environment. When I import the squidpy, an import error occurred : `ImportError: cannot import name 'get_cmap' from 'matplotlib.cm'`
## Minima…