Best method to do clustering (sub-group) single cell RNA-Seq data?

Question

[sudha]

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

Answer 1

[ZZzzzzhong]

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

Answer 2

[chris86]

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

Answer 3

[Kristoffer Vitting-Seerup]

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