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!
Hopefully you have already seen the Galaxy scRNA-seq tutorials, but if not find them here:
This specific tutorial might be enough