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When I run
` STPreProcess(InDir = InDir, OutDir = OutDir, Sample = Sample)`
It throws the following error:
```
Error in initialize(value, ...) :
invalid name for slot of class “Assay5”:…
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hello, thank you for making this great tool. I cannot seem to understand how to use it.
I have differentially expressed genes from findmarkers() in seurat between diseased fibroblasts and control fi…
Flu09 updated
1 month ago
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This additional function is necessary if SCTransform was used, otherwise we won't find any markers. We need to read a bit more on this. For now, I added the following code, just above `RunPrestoAll`:
…
ktrns updated
2 weeks ago
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Hi, @rcorces @jeffmgranja @jgranja24 @keyuxi
I would llke to copy my entire ARCHR project cluster, embedding, umap ... into a seurat object but I do not succed to copy embeddings
I try many thi…
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Hi,
Love your package and hope to continue using it!
I believe `SCpubr` has support for `Seuratv5` but I was having some trouble with the `do_DimPlot` function. Am I missing something?
```
…
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Hi,
Thank you for an amazing package. I was successfully able to run this on my other seurat objects but not with this one. Is it the version issue? Following is the error:
```
query.projected
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Hi!
First off, thank you for this analysis tool!
I am analyzing some Perturb-Seq data and have followed the vignette. I ran Mixscale_Scatterplot and interestingly the perturbation score seems p…
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Hi,
I have a seurat object containing 6 samples(seurat v4), I performed integration to correct batch effect-following [https://satijalab.org/seurat/articles/integration_introduction.html](url). Now I…
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Hello, there is a minor issue with the output from CytoTRACE2.
**The problem is that the clustering appears upside down.**
![outputs](https://github.com/user-attachments/assets/fd1ac053-3182-4d38…
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Dear Prof. Fan,
Thank you again for developing this useful package!
I encounted 'Error in shape[k]