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ilee8
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@ilee8-20930
Last seen 4.5 years ago
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?
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.