entation were used as features of each cell; <strong>4)</strong> On latent representations, graph clustering was used to identify cell groups that were close in the latent space; <strong>5)</strong> Based on cell clusters, we could further perform differential analysis on either morphological and transcriptional modality, to identify different cell properties.</p>
<p>Detailed introduction for each step was provided in the notebook.</p>
<h2 id="depdendency-of-running-the-code">Depdendency of running the code