DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
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ilee8 • 0
@ilee8-20930
Last seen 13 months 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?

scRNA-seq Seurat DE • 917 views
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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.

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Aaron Lun ★ 27k
@alun
Last seen 17 hours ago
The city by the bay

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

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