Question: Getting the cells from the clusters Seurat has found
gravatar for suvratha
5 weeks ago by
Institute of Bioinformatics and Applied Biotechnology
suvratha40 wrote:

Hello, I've been using Seurat v3.1 for single-cell analysis of mouse data. I've clustered the cells and Seurat has found 12 different clusters for my data. Now, I need to name the clusters so that I know which particular cell type has clustered where on the UMAP plot. Is there any other way to do this other than using the FindMarkers() function and then naming them based on the most differentially expressed gene in the cluster? Also, is there a way to retrieve the data where we know which cell/data has gone into the UMAP predicted cluster so that I can at least I know which cell type has gone where in the plot based on a metadata file I have for my data?

Thank you.

single cell seurat rna-seq R • 122 views
ADD COMMENTlink modified 11 days ago by Evan20 • written 5 weeks ago by suvratha40

you can plot the known marker gene to check the cluster.

ADD REPLYlink written 5 weeks ago by shoujun.gu280
gravatar for Evan
11 days ago by
Evan20 wrote:

Hello, I got approximately the same question recently and I succeed to find the answer. Here is the command in Seurat to get a file with two columns, one with cell sequence and a second column with associated cluster. Each line of this file will be one cell.

write.table(yourdata@active.ident, file='Cell_Cluster.tsv', quote=FALSE, sep='\t', col.names = FALSE)
ADD COMMENTlink modified 11 days ago • written 11 days ago by Evan20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 799 users visited in the last hour