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Hi, trying to run `FindAllMarkers` on SCT transformed data:
```
# find markers for each cluster
seu
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Hi there,
I have been running an analysis in Seurat 5 that is partially run on a local machine and a remote server.
As my Seurat objects were created remotely using `write_matrix_dir()`, after m…
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Hi,
I have precomputed seurat objects. Can I use these objects? or any example?
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# Background
rds objects downloaded from Cellenics contain EnsemblIDs as rownames (as default and most prevalent case), with the gene symbols stored in the `@misc$gene_annotations` slot.
This impli…
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**I have multiple samples from various GEO datasets that need batch correction. Currently, I've created five Seurat objects in Seurat V5 and merged them into a single object. I would like to perform t…
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Hello again
Sorry to bother you but I tried to run Scarlink with my own data this time (work perfectly with yours). I'm working on Rat samples, so I runned the preprocessing with a Rat GTF file (the …
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Add documentation explaining features that don't work in either of the three object formats. For example, SingleCellExperiment objects don't support subsetting based on feature expression, or differen…
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Hi,
I had another question. are you guys planning to update your code to take CITE-seq Seurat objects created with Seurat V3 or later?
Thanks,
Andrew
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Hi there,
Congrats on a great work, and thanks for developing this package.
I am attempting to pull TCR-seq data for T cells that also have the GEX/CITE-seq Seurat objects.
**QUESTION 1.** …
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Hello everyone.
Im having some trouble loading data into the web app of Azimuth. Previously in RStudio Ive created a RDS file and then try to loading it into Azimuth but it throws the following er…