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Hi, when running the shiny app I try to set my own annotations as default but the original data's annotations (clusters 1-12 and layers 1-6) still show in the cluster static. I tried loading them ag…
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hello!
when I followed your vignette for getting Human DLPFC Visium dataset (https://bioconductor.org/packages/release/data/experiment/vignettes/spatialLIBD/inst/doc/spatialLIBD.html#downloading-the…
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As you said before (#35), I downloaded the three files manually: modeling_results, sce, sce_layer. But when I tried to convert sce to spe object, error happened. I used check_sce(), there was the same…
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Hi @ellispatrick
thanks for the great tool! I'm now at the visualization part and would like to set a cutoff on the adjusted rather than the raw p value.
My expectation is that
```
data(spic…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/lmweber/smoothclust
Confirm the following by edit…
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```r
DotPlot(pbmc, features = c("MS4A1", "GNLY", "CD3E",
"CD14", "FCER1A", "FCGR3A",
"LYZ", "PPBP", "CD8A"),
group.by = 'seurat_clus…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ChenLaboratory/scider
Confirm the following by ed…
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I'm working through some fixed/updates to the [OSCA books](https://osca.bioconductor.org/), where **MouseGastrulationData** is used in quite a few places.
I've noticed many (all?) of the count matric…
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Hello, I'm the package maintainer of [SpotClean](https://github.com/zijianni/SpotClean). I'm getting errors under Seurat v5 but not v4 when maintaining my package. Below should be a simple reproducibl…
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Should be super easy. The harder part is to add Xenium toy dataset for unit testing.