Best method to do clustering (sub-group) single cell RNA-Seq data?
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
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Kristoffer Vitting-Seerup
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sudha •
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sudha •
3 answers
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
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ZZzzzzhong
The only benchmark I'm aware of is this - and according to it Seurat and SC3 are the better options.
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Kristoffer Vitting-Seerup
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