Question: Best method to do clustering (sub-group) single cell RNA-Seq data?
0
gravatar for sudha
12 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 • 653 views
ADD COMMENTlink modified 12 weeks ago by kristoffer.vittingseerup1.4k • written 12 months ago by sudha20
1
gravatar for ZZzzzzhong
7 months ago by
ZZzzzzhong190
ZZzzzzhong190 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 7 months ago by ZZzzzzhong190
0
gravatar for chris86
12 weeks ago by
chris86220
United Kingdom, London
chris86220 wrote:

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

ADD COMMENTlink written 12 weeks ago by chris86220
0
gravatar for kristoffer.vittingseerup
12 weeks ago by
European Union
kristoffer.vittingseerup1.4k wrote:

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

ADD COMMENTlink written 12 weeks ago by kristoffer.vittingseerup1.4k
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