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It looks like `spotclean` is relying on `SpatialExperiment::spatialData` for pulling various data from a `SpatialExperiment` object, but `spatialData` is now deprecated and when I run `spotclean` I ge…
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Hi, could you please inform where can I find the Visium data in your paper? Thanks~
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I wanted to load a filtered data from a spatial 10X experiment by:
`se
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In addition to `SingleCellExperiment`, make all datasets available as `SpatialExperiment` class objects.
https://bioconductor.org/packages/devel/bioc/html/SpatialExperiment.html
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Hello! Thank you for creating this amazing package. I was wondering whether BayesSpace provides a way to subset cells in enhanced SCE based on expression-level conditions of multiple genes/features.
…
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if (!exists("spe"))
spe
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StartracDiversity(immuneTCRgene, type = "Cancer", sample = "patientNumber", by = "overall")
[2023-12-17 21:13:42.644434] initialize Startrac ...
Error in (function (cl, name, valueClass) :
as…
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Because the `PRECAST` pipeline is based on `Seurat`, which creates difficulty for bio conductor users who's familiar with `spatialExperiment`.
I wrote these wrapper functions to convert a spatialEx…
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I am having this issue of my jupyter notebook not being able to find the GenomeInfoDbData package even though it is already installed in my conda environment. Note: I am trying to use this package as …
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It would be great if I could hand the wrapper function a sce or spe and just specifiy the assay to use.
Hopefully it outputs the cellType clusters in a colData