Seurat -Find conserved cluster markers and DE genes in two samples

Description

This tool gives you

The cell type markers that are conserved across conditions (conserved_markers.tsv)
The differentially expressed genes between the conditions (de-list.tsv)

for a given cluster. "Conditions" are the ones determined in the Setup tool with the Sample or group name parameter. This tool can be used for two sample combined Seurat objects.

Parameters

Name of the cluster [3]

Details

As inputs, give the combined Seurat object.

Select the cluster you want to inspect by setting its name in the parameter field. As an example, the parameter is set to cluster "3".

conserved_markers.tsv is a matrix containing a ranked list of putative conserved markers, and associated statistics: p-values within each group and a combined p-value (such as Fishers combined p-value or others from the MetaDE package), percentage of cells expressing the marker and average differences.

For more details, please check the Seurat tutorials for multiple sample analysis.

Output

conserved_markers.tsv: Conserved cell type markers across the conditions
de-list.tsv: Differentially expressed genes between the conditions