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All scCustomize/Nebulosa Plots are not printing to my R version. If I use ggplot2 versions > 3.4.4 I receive this error:
Error in `Plot_Density_Custom()`:
! Due to error in Nebulosa package and …
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Hi Josep,
at one point during "Run.HiTME", the ref maps used get saved to obj@misc (see reference to specific line of code below).
https://github.com/carmonalab/HiTME/blob/57fb29505ffac0598ee47…
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Hello, I have 5 class.
first read count matrix,normalize,findvariablefeature and then use merge instruction for merge seurat object of each class.
second I want Integrate different class. why do w…
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Hi,
I followed the instructions in https://ncborcherding.github.io/vignettes/vignette.html as follows:
```
> library(scRepertoire)
library(Seurat)
Loading required package: ggplot2
Attaching…
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Hey Tim,
Thanks for creating such a useful tool for analyzing scATAC data.
You recently helped out with successfully linking peaks to genes on a merged object that followed the [merge](https:/…
wht10 updated
8 months ago
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Dear Seurat team,
I am using the beta version of Seurat v5 and noticed that the newly added function parameter `destdir` in `saveRDS()` (which previously worked without an issue), doesn't work anymor…
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Hi,
Thanks for the wonderful tool.
I have used it for my previous projects and it indeed was very helpful.
Lately, I have started using Seurat 5 where RNA assay has "data" inside "layer" slot which…
anksi updated
10 months ago
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Thank you for developing such a wonderful tool. I have run CytoSPACE successfully on Visium data. I would like to create either a Seurat or SingleCellExperiment object using the assigned_expression an…
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Hi!! I have a question concerning anlysisis in Seuratv5.
From the tutorial, it says that Ther is no need anymore to merge two or more seurat objects normalized, scaled, etc. (I mean, there is no need…
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Hello,
I am confused about how to best prepare a Seurat object for Velocyto after integration. I have been able to run both velocyto and scvelo by taking the loom file created via standard velocyto…