HighOrder_SComparison is an R package for detecting differenital genes associated with phenotype from single cell profiles. This tool is developed and maintained by Ken chen's lab in MDACC. There is a pressing need for computatinal tools to enable the detection of genes associated with phenotypes in single-cell level. This task is very challening in single-cell studies due to the existence of: 1) changes in cell type composition among samples and 2) unknow technological batch effects. The proposed high-order gene detection method first leverages the canonical correlation analysis (CCA) to align cell populations from two sample into shared space, and then detects gene changed in each latent space. The gene difference in latent spaces are finally aggregated into the population-level mismatching score, which can capture gene change due to subtle cell states.
