Question: Best method to do clustering (sub-group) single cell RNA-Seq data?
0
gravatar for sudha
9 months ago by
sudha20
sudha20 wrote:

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 • 523 views
ADD COMMENTlink modified 15 days ago by kristoffer.vittingseerup1000 • written 9 months ago by sudha20
1
gravatar for ZZzzzzhong
4 months ago by
ZZzzzzhong120
ZZzzzzhong120 wrote:

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 COMMENTlink written 4 months ago by ZZzzzzhong120
0
gravatar for chris86
17 days ago by
chris86200
United Kingdom, London, UCL
chris86200 wrote:

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

ADD COMMENTlink written 17 days ago by chris86200
0
gravatar for kristoffer.vittingseerup
15 days ago by
European Union
kristoffer.vittingseerup1000 wrote:

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

ADD COMMENTlink written 15 days ago by kristoffer.vittingseerup1000
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1285 users visited in the last hour