Question: Can EdgeR of DeSeq be used for Single-cell RNA-seq?
gravatar for neja
5.9 years ago by
neja30 wrote:

Hi all,

I've a single-cell rna-seq data and need identify DE genes across different cell groups. I would like to know can we use edgeR of DESeq for DE analysis of single-cells? If yes, then do we use the cells of the same group as replicates?

Thanks in advance!


rna-seq • 5.5k views
ADD COMMENTlink modified 5.9 years ago by dariober11k • written 5.9 years ago by neja30

Use monocle for single-cell RNA-seq

ADD REPLYlink modified 5 months ago by RamRS26k • written 5.9 years ago by Ming Tang2.6k

Thanks dariober for your response.

I'm aware of Monocle and am currently using it. But what I wanted to know is that can the standard RNA-seq tools be used for single-cell RNA-seq?Are there no specific requirements for single-cell rna-seq in terms of normalization etc, given that single-cell has the information of a single transcriptome whereas the standard rna-seq gives the average expression pattern of a cell-population.

ADD REPLYlink written 5.9 years ago by neja30
gravatar for dariober
5.9 years ago by
WCIP | Glasgow | UK
dariober11k wrote:

I would say yes, you can look for differential expression from single cell RNA-Seq. In the end edger/DEseq don't care where your counts come from.

About your second question, it's up to you to decide which sets of libraries to contrast to look for DE. Comparing cells from one group vs cells from another group seems sensible if your are intersted in the differences between groups.

ADD COMMENTlink written 5.9 years ago by dariober11k

I found Deseq2 used in package Seurat

ADD REPLYlink written 18 months ago by linouhao0
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