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Hi, I have an object with 1.1mil cells across 200 samples. I've used Seurat's BPCells method to minimize the amount of processing done in-memory. However, when I try to run `AddModuleScore_UCell`, I g…
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Hello I use the code from "Running scGSEA from gficf on Seurat Objects" (docs/scGSEA.Rmd). But when I run runScGSEA function I get this error:
> pbmc.ptw | >
>
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**Description:**
The current implementation of the `CreateNicheDEObjectFromSeurat` lacks support for converting the Seurat 10X Xenium object to the niche-DE format. As a result, users are unable to…
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Hi,
I am trying to use conos to integrate 18 samples and the workflow fails at the conversion step from conos to Seurat:
```
seurat.merged
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Hi,
I am working with a very larger sc/sn RNA-Seq dataset. Starting from an h5ad file have used BPcells package to load data in-memory as follows:
`raw
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Hi,
Wonderful job!
I have searched through many articles and am looking for a Shiny app that can handle spatial transcriptomics data in a similar manner to how [Shinycell](https://github.com/SGDDN…
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AnnData --> Seurat, particularly now there is Seurat v4 trajectory stuff/automated annotation stuff/Monocl can import Seurat objects... this is important!
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Some tools currently in Scanpy need Seurat versions to make Seurat tools usable for researchers, which would be helpful given that stuff like Monocl/cell annotation/etc. are more available with R obje…
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```r
# insert reproducible example here
I have 5 samples for xenium assay, and want to analyze them in r by integrating them together. after that, i want to split them by using split…
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Hi,
I am working with a very larger sc/sn RNA-Seq dataset. Starting from an h5ad file have used BPcells package to load data in-memory as follows:
`raw