How to isolate and analyze subclusters from an initial scRNAseq cluster

Hi everyone,
I was able to successfully cluster scRNAseq data from this recent paper " Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer" in which I was able to identify several different colonic epithelial cell clusters of interest. I considered increasing the resolution of the initial clustering to get more specific epithelial subgroups, but because the annotation of clusters must be done manually, I found it difficult to label the large number of clusters that resulted from the increased resolution. Because I am only interested in further investigating the epithelial clusters and do not wish to look into smaller groups of stromal or immune cells, I was wondering if there was a way to isolate and interrogate just certain clusters from the original dataset and perform downstream subsetting on those specific clusters. Hope that makes sense!

Hi @jesskope13

Hopefully you have already seen the Galaxy scRNA-seq tutorials, but if not find them here:

This specific tutorial might be enough