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Hi all,
I've been testing the use of cell2cell and MOFA within Liana and was wondering if there was a way to use the ligand-receptor information from the spatial bivariate vignette instead of rank…
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Hi,
what does the parameter mean when build spatial neighborhood graph (https://squidpy.readthedocs.io/en/stable/_modules/squidpy/gr/_build.html#spatial_neighbors)?
![image](https://github.com/scver…
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Hi everyone,
I analyzed Visium spatial transcriptomics data using squidpy.
When using "spatial_scatter", is it possible to not show specific dots with a gene expression leven below a certain t…
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Following the same jupyter notebook (tutorial_visium_hne.ipynb) with the same tutorial data but got the following error:
---------------------------------------------------------------------------
V…
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Hello, I have a question about this tutorial: https://squidpy.readthedocs.io/en/latest/notebooks/examples/plotting/plot_segment.html. In this tutorial, you have plotted fibroblast and epithelial clust…
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Breaking change between `anndata 0.10` and prior versions means that some of our tools running `anndata 0.7-0.8` are incompatible with tool suites that run `anndata 0.10`, resulting in the following e…
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Thank you for developing such a valuable tool!
I have a question regarding the logic behind this line of code (https://github.com/scverse/squidpy/blame/ecee104bd165921f7a48934c13ff95599405e3eb/src/…
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Hi,
I am receiving the error below when I am loading in Nanostring data. And I found that if I delete the imge folder ("CellComposite", "CellOverlay") and only keep the exprMat, matadata and fo…
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### Description of feature
Apparently this is a thing now (e.g. 10x spatial transcriptomics + mixcr, e.g. in [this paper](https://www.sciencedirect.com/science/article/pii/S1074761322000814?via%3Dihu…
grst updated
2 months ago
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There should be tutorials giving a general introudction to
* spatial anlaysis with squidpy
* how to use spatialdata
grst updated
11 months ago