Question: DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
0
gravatar for ilee8
9 weeks ago by
ilee80
ilee80 wrote:

I have a set of 10X scRNA-seq data from 8 samples which include 4 biological replicates for each of the 2 conditions. The samples were processed in 3 days - 1 control sample on the first day, 1 control and 2 treated samples on the second day, and 2 control and 2 treated samples on the third day. I have used the Seurat pipeline to integrate the dataset and cluster the cells. What is the best way to model this for differential expression analysis between conditions?

de seurat scrna-seq • 176 views
ADD COMMENTlink modified 9 weeks ago by Aaron Lun25k • written 9 weeks ago by ilee80

Seurat is not a Bioconductor package. To ask questions about Seurat see

Seurat provides does provide DE functions. There are Bioconductor functions for DE analysis of course but I'm not sure that they would be able to use the Seurat preprocessing that you have already done.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Gordon Smyth39k
Answer: DE analysis for 10X scRNA-seq data with multiple conditions and multiple replica
2
gravatar for Aaron Lun
9 weeks ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

https://osca.bioconductor.org/multi-sample-comparisons.html

ADD COMMENTlink written 9 weeks ago by Aaron Lun25k
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