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Hello, I want to use scATAC-seq dataset to deconvolute 10x Visium dataset, is it feasible?
When I prepare anndata for the regression model, some warings appeared as follows:
cell2location.models.R…
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Routinely listing improvement we can make to the docs:
- [x] add `rasterize_bins()` example in Visium HD notebook;
- [ ] show how to use `get_element_instances()` in the annotation notebook.
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Two of the visium readers' inputs are `fullres_image_file` and `scalefactors_file`.
Some of the visium dbs (below) have multiple subfolders/types in their ./spatial subfolder, each with their own di…
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Hello, I am trying Seurat for the latest visium HD data and trying to use SpatialFeaturePlot function. I used the exact same script shown in vignette for preprocessing, but the feature plot is just H&…
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Thank you very much for `bin2cell`.
@ktpolanski is `b2c.view_labels()` in 0.3.2 the unformalized custom function @nadavyayon referred to and was using at 18 minutes and 35 seconds (18:35) in the Se…
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Great package!
However, I encountered a bug when executing the manual_gross_alignment, which caused a crash of my jupyter kernel. Could you help me fix it?
Thanks a lot~
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Hi, Nice work it is!
Is this applicable for 10x visium data?
Thanks!
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[combineMetadata](https://drieslab.github.io/GiottoClass/reference/combineMetadata.html)(visium_kidney)
# select annotations, reductions and expression values to view in Giotto Viewer
viewer_folde…
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Hello,
Your approach looks very interesting! And I hope your pre-print will get accepted.
I would like to run xfuse on GPU cluster using one dataset from Visium. Few questions:
- does one need t…