Question: Best method to do clustering (sub-group) single cell RNA-Seq data?
0
gravatar for sudha
18 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 • 922 views
ADD COMMENTlink modified 8 months ago by kristoffer.vittingseerup2.2k • written 18 months ago by sudha20
1
gravatar for ZZzzzzhong
12 months ago by
ZZzzzzhong200
ZZzzzzhong200 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 12 months ago by ZZzzzzhong200
0
gravatar for chris86
8 months ago by
chris86290
United Kingdom, London
chris86290 wrote:

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

ADD COMMENTlink written 8 months ago by chris86290
0
gravatar for kristoffer.vittingseerup
8 months ago by
European Union
kristoffer.vittingseerup2.2k wrote:

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

ADD COMMENTlink written 8 months ago by kristoffer.vittingseerup2.2k
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