satijalab / integration2019 Goto Github PK

The download link does not exist
curl -L https://www.dropbox.com/s/m390vmhnabti4bl/matrix_doublets.tsv?dl=0
--create-dirs -o raw_data/10x_scrna/pbmc10k_v3/matrix_doublets.tsv
can you restore the link?
Thanks a lot!

Hi,

Are the final processed data files with cell type annotations for the bone marrow CITE-seq dataset available somewhere (perhaps as a saved Seurat object)?

Thanks,
Keshav

Hello,

MixingMetric was calculated by MixingMetric function or by max.k-MixingMetric().
As what I understood, MixingMetric() will return the final result.
but, the code in your script is mm = max.k - MixingMetric .
Could you tell me how should I use this function?

Thanks,
Jialu

About "pbmc_10k_v3.rds",
The download link of that is broken.
I can't repeat your process strating from UMI matrix, but I need the annotation of cell type in "pbmc_10k_v3", can you restore the link or send this file to me by email?

Thanks so much!

Hello,

I have posted about this before, but I'm still having trouble. I am trying to see which genes are most different between my conditions in one cluster. Here is my code and error.

svzyoung$celltype.gender <- paste(Idents(svzyoung), svzyoung$orig.ident, sep = "&")
svzyoung$celltype.gender <- Idents(svzyoung)
Idents(svzyoung) <- "celltype.gender"
diff.gender.astro <- FindMarkers(svzyoung, ident.1 = "Astro&SVZ_Young_Female", ident.2 = "Astro&SVZ_Young_Male", verbose = FALSE)
head(diff.gender.astro, n = 15)

Error in WhichCells.Seurat(object = object, idents = ident.1) :
Cannot find the following identities in the object: Astro&SVZ_Young_Female

I have tried sep="_" as well.