stering of cells towards one sample (i.e., a “batch effect”), which could cause spurious disease enrichment in the mixed effect model. Since Signac classifies each cell independently (without using clusters), Signac annotations can be used with MASC without a priori balancing samples or cells, unlike cluster-based annotation methods.</li>
</ul>
<p>This vignette shows how to use SignacX with Seurat and MASC. There are three parts: Seurat, SignacX and then MASC. We use an example data set of kidney cells 