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Hello there,
I have been using BANKSY for each sample separately on Xenium data but I was wondering if there was a way to do the multisample analysis on seurat object as well or not? by converti…
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Hello,
I ran `BayesSpace` with k = 28 for ~113,000 spots. I've noticed that I only get 26 clusters because clusters 18 and 21 are missing. Is this to be expected? Is it possible, `BayesSpace` is m…
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Hi all,
I'm starting to use `SpatialData `framework but I'm still missing something.
I'm working on this [public CosMx dataset](https://kero.hgc.jp/Breast_Cancer_Spatial.html). I'm able to read it a…
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Hello,
I'm running into an issue running concordexR on my dataset. I'm running with just loading the metadata, trying to follow the example code from [the liver dataset in the biorxiv github](https…
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Hi Ryan,
I believe that either https://github.com/LieberInstitute/spatial_hpc/blob/main/code/11_iSEE_apps/pseudobulk_iSEE or https://github.com/LieberInstitute/spatial_hpc/tree/main/code/11_iSEE_ap…
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Hi,
While using `BayesSpace` version 1.4.1, I'm running `spatialEnhance()` on a dataset with the following dimensions:
```R
> dim(spe)
[1] 27853 38115
```
with it, I get the following erro…
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Hello,
I wanted to reproduce the vignette "Introduction to scRNA-seq integration" (https://satijalab.org/seurat/articles/integration_introduction)
and I ran into an issue when trying to load the…
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When trying to run app.R, I get the following warnings which do not allow me proceed:
Need SpatialExperiment >= 1.1.5 but loaded version is 1.0.0
2: object ‘imgData
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Please ask questions about how to use `spatialLIBD` on the
[Bioconductor Support Site](https://support.bioconductor.org) using the
appropriate tag(s) including the one for this package.
**Note**.…
hym97 updated
2 months ago
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Hi,
Banksy has worked well for me on individual samples and returned interesting results compared to traditional clustering. I am now interested in comparing the clustering results using Banksy on…