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It was a nice job. I came for the Seurat object, but I noticed that the plop.txt file within the seurat_object folder is empty. Could you kindly provide a link for downloading? Thanks
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Hello, I am trying to replicate your simulation described in the manuscript.
I generated single cell data using Splatter with the following parameters:
parameters
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this is my object,
colnames(seurat.obj@meta.data)
[1] "orig.ident" "nCount_RNA" "nFeature_RNA"
[4] "percent.mt" "DF.classifications" "S.Score" …
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Hello! Thanks a lot for your great package CASCAM! Unfortunately it is not working for me. This is how I call the Celligner function:
`seur_celligner
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Hi Jan,
I am using SPATA2 on a Xenium dataset and used createGroupAnnotations to create the spatial annotation. However, I noticed that the outlines do not capture all the groups I want. In the i…
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Similiar to the discussion in https://github.com/theislab/zellkonverter/issues/34
A lot of tools like https://github.com/immunogenomics/presto/ will try to call functions from the Matrix package tha…
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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
2 months ago
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### Report
Hello,
We (@jameshyojaelee) are running PertPy Mixscape vs Mixscape with the same parameters and we are getting very different results -- PertPy is calling more perturbed cells than Mixsc…