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Hi，great to see the new version!
I followed the tutorial to do it, but when using plotData, the following error occurred. Do you know what's going on?
`library(CytoTRACE2)`
`expression_data
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I am having troubles with data conversion into a Seurat (or RDS) when I rerun segmentation.
I start with a D02168B3.adjusted.cellbin.gef and run
`conda activate stereopy3_8
python
import ste…
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Hi,
I was looking into the vignette script you provided for the Thrane melanoma dataset and especially how to do the DE analysis
using the seurat_cluster_DE function (http://www.ezstatconsulting.c…
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library(irGSEA)
library(Seurat)
Loading required package: SeuratObject
Loading required package: sp
‘SeuratObject’ was built under R 4.3.0 but the current version is 4.4.0;
it is recomended that …
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Thank you very much for the wonderful tools!
I am now working with Visium HD data and would like to use seurat for some of the analysis after cell segmentation. May I ask how you suggest to conve…
LinAU updated
2 weeks ago
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Dan S has a method for making RunUMAP reproducible across different machines. He is trying to submit a pull request to get this incorporated into Seurat. In short it involves implementation of the app…
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It would be better if there was a convenient function to convert seurat to anndata.
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I hope this message finds you well. I am currently working with your package (likely SPATA2 or another spatial transcriptomics-related package) and encountered an issue when attempting to use the asMo…
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**Intro**
- Leiden clustering clustering based on KNN graphs and UMAP can sometimes leave stray cells assigned to clusters that are visually or spatially distant on the UMAP.
- These scattered cell…
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Hi, I intend to convert a h5ad file to seurat data. The code is:
library(anndataR)
adata