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


For a given cluster this tool gives you

Conditions are determined in the Setup tool with the Sample or Group name parameter.



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".

You can filter both the conserved marker genes and the differentially expressed genes using the parameters. By default, only genes with adjusted p-value < 0.05 are listed in the result table and only positive markers are kept. Note that Seurat adjusts p-values using the rather conserved Bonferroni method for multiple testing correction.

You can choose to include in the analysis only genes whose average fold change is higher than a selected value. This prefiltering speeds up the analysis and narrows down the result list. Note that Seurat calculates fold change in ln scale (log base e), so if you are interested in two-fold expression changes in linear scale, you need to enter 0.693 in the parameter.

The result table de-list.tsv contains the genes which are differentially expressed between the two conditions in the selected cluster. The columns include

conserved_markers.tsv contains a ranked list of conserved marker genes for the chosen cluster (= genes that show specific expression in this particular cell type/cluster, regardless of the treatment). In addition to the columns listed above, this table contains also the following columns:

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