Best method to do clustering (sub-group) single cell RNA-Seq data?
3
0
Entering edit mode
3.8 years ago
sudha ▴ 20

Hi Dear one,

I have 50 single cell RNA seq data of neuronal cells, I want to find the differential gene expression between the sub groups!

As for now I have calculated expression counts (in gene and isoform level) using RSEM ( I am planning to use EBSeq for differential gene expression), Can anyone guide me to do subgrouping (clustering) from this RSEM output? or any other best way?

thanks in advance

RNA-Seq rna rna-seq • 1.9k views
ADD COMMENT
1
Entering edit mode
3.4 years ago
ZZzzzzhong ▴ 240

you can try Seurat(https://satijalab.org/seurat/pbmc3k_tutorial.html).it only need the genecount matrix,then you could do clustering ,DE,and so on

ADD COMMENT
0
Entering edit mode
3.0 years ago
chris86 ▴ 370

Seurat is good, I have also found SC3 effective and MUDAN.

ADD COMMENT
0
Entering edit mode
3.0 years ago

The only benchmark I'm aware of is this - and according to it Seurat and SC3 are the better options.

ADD COMMENT

Login before adding your answer.

Traffic: 2599 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