Consider a single cell RNA seq data with a control and a test sample. These are integrated to minimize the batch effect. Reads have been normalized to the sequencing depth. One can compare the samples for their cluster composition. Further one can perform cluster-wise differential expression followed by enrichment analysis to find out genes and pathways up or down regulated in the samples. One may also perform trajectory analysis to study transition between cell types.
Apart from this, are there any ways to compare and find differences between samples in a single cell RNA seq data? I am looking for methods/tools/parameters that can tell me differences if any between the samples particularly in the absence of any hypothesis (even if I have a hypothesis in mind, I would still be interested in unbiased way of finding differences between the samples)