Samuel Marsh

Hi, Not member of dev team but hopefully can be helpful. What are the results of this code both before and after you rename the rownames. `head(rownames(x = E.data[["Antibody Capture"]]),...

Hi, Not member of dev team but hopefully can be helpful. This is issue only with the old visualization style for split violins. See response from dev team here: https://github.com/satijalab/seurat/issues/3007#issuecomment-629310216...

Hi, Not member of dev team but hopefully can be helpful. According to code you pasted above OBJ_meta is a dataframe: `OBJ_meta % select(orig.ident) %>% rownames_to_column("barcodes")` Therefore, you can plot...

Hi, Not member of dev team but hopefully can be helpful. Can you please provide full code that you are running for the analysis and the code you are using...

Can you post the code and output of the comparison are you running that states that counts after are different?

Hi @Huimin721 So the issue you seem to be describing in this last post is not about the raw counts changing after RPCA (or any analysis) but the `OBJECT[['RNA']]@counts` being...

Hi @Huimin721, So I think what you are describing is still object creation issue. I didn't see 10X files in repo you posted so I just used one of mine...

Hi @Huimin721 I'll leave that to @yuhanH or another member of the Seurat team in terms of analysis methods behind integration. Best, Sam

Hi, Not member of dev team but hopefully this is helpful. So this isn't really a LIGER issue if you are running LIGER through the Seurat wrapper and using future...

As another option I have created package scCustomize that also has some Liger functionality. I have adapted the internal Liger plotting to support Seurat like arguments including `split.by`. You can...