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Hi, I had a read of you preprint and think that SpaNorm looks like a great tool to test on some MERSCOPE and Xenium data I am currently analyzing. I was wondering whether the SpaNorm package can work …
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Hi,
Is there an available script for preparing Seurat data for batch preprosessing of count data in jupyter notebook?
I am running the cNMF code from R and would like to see if there is a batch …
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Hi,
Is the reference Seurat object available somewhere? I would like to run TCellMap.R.
refSeuratObj
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Hi,
I've been testing CellScopes with various spatial transcriptomics datasets and find its capabilities very impressive. However, I encountered an issue when trying to subset CellScopes objects.
…
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Is it possible to cluster cells in seurat data object (count data) with scVAE?
Is it possible to apply it on scaled data? Like if cell types are already regressed out from gene expressions?
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**Describe the bug**
I am trying to run vitessceR using Seurat v5 objects as input. I get the following error:
```
Warning: Overwriting previous file data/seuratdata/A/0/seurat.zarr.h5Seurat
Crea…
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Is it possible to turn the cpp pointer back into R?
Now `logNormCounts.chan` return a `pointer` contaning the logcounts matrix, which makes it hard to integrate with `Seurat` or `SingleCellExperime…
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Dear CellScopes team,
Hello! I have always admired your team's outstanding publications in kidney research. Recently, I tested CellScopes, and I must say it is truly impressive. I was amazed by its a…
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thanks for developing loupeR, has worked great for all my Seurat objects to help share data to others
however, i have a seurat object where our collaborator removed doublets with 'singleCellTK'; ho…
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I was trying to create a reproducible example of another issue I'm having with JoinLayers() taking an indefinite amount of time (killed manually after ~12 hours).
The dataset I used is from [here](…