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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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Hello,
I have been trying to convert SPATA objects from the SPATA data using downloadSpataObjects function. I am able to download the data/RDS files fine. When I load them in with and try to conver…
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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, I'm trying to analyse 18 samples of public 10x Spatial data, using Seurat 5. My goal was to perform SCTransform on each sample, merge them, and eliminate batch effect of different slide (that was …
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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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Hi, I wanted to first and foremost express my appreciation for this fantastic package!
I am trying to apply the TF activity inference functions on my 10X scRNA-seq data. For reference, my dataset …
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Hello there,
Thank you for developing CSS! We are trying to use it on a set of Seurat objects created via Seurat_V5.
Basically, I have 2 Seurat objects each from a separate experiment. I merge…
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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…