Reproducible seurat clustering
0
0
Entering edit mode
13 months ago
synat.keam ▴ 100

Dear all fellows,

What is the standard way for reproducible Seurat clustering in single cell? I have been trying to use set.seed function like

library(tidyverse)
library(Seurat)
library(patchwork)
set.seed(198752)

However, once it comes to running the following script, I get new shape of cluster all the time I rerun it. How to make it reproducible because I am planning to use it for publication.

All_arthritis_integration_UMAP<- RunHarmony(All_arthritis_normal, group.by.vars = "orig.ident")
All_arthritis_integration_UMAP <- FindNeighbors(All_arthritis_integration_UMAP, reduction= "harmony", dims = 1:40)
All_arthritis_integration_UMAP <- FindClusters(All_arthritis_integration_UMAP, resolution = 0.2)
All_arthritis_integration_UMAP <- RunUMAP(All_arthritis_integration_UMAP, reduction = "harmony", dims = 1:40,
                                   n.neighbors = 30, min.dist = 0.4, spread =3)
`

Also, I would like to ask whether I could adjust some parameters in RunUmap to make cluster look better by trying some parameters like n.neighbors= XX, min.dist= XX, spread= XXX because if I run the default function, the clusters in my data looks messy.

Kind Regards,
Synat

seurat clustering single-cell • 716 views
ADD COMMENT
0
Entering edit mode

set.seed(198###) #I've redacted a part of it

Is that your birthday? Be careful on the web, my friend!

ADD REPLY
0
Entering edit mode

not my birthday. thanks

ADD REPLY
0
Entering edit mode

Nice. Glad to know. I'll delete my comment in a bit.

ADD REPLY

Login before adding your answer.

Traffic: 1701 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6