Seurat -Extract cells in a cluster

Description

This tool gives you a subset of the data: only those cells in a user defined cluster.

Parameters

• Name of the cluster [3]

Details

As inputs, give the Seurat object created AFTER clustering step: either after

• Seurat v3 -Clustering and detection of cluster marker genes tool,
• or after Seurat v3 -Integrated analysis of two samples tool in case of two sample analysis.

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 continue analysing this subsetted R-object by running the Seurat tools again; in the case you started with a single sample (subsetting after Seurat v3 -Clustering and detection of cluster marker genes tool), you can start with the filtering and finding variable genes, and continue from there.
If you started with a combined Seurat object of two samples (subsetting after Seurat v3 -Integrated analysis of two samples tool), you can continue by running the after Seurat v3 -Integrated analysis of two samples tool again.

Note that the cell filtering (number of genes per cell, mito%) done in the original dataset effect this object as well.

Output

• seurat_obj_subset.Robj: The Seurat R-object containing only the cells in the chosen clustesr. Can be passed to the next Seurat tool, or imported to R. Not viewable in Chipster.
• QCplots.pdf: Quality control plots (similar to the ones in Setup tool.)