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We used the van Elteren test implementation for Seurat objects (https://github.com/KChen-lab/stratified-tests-for-seurat) to detect marker genes for each node of the cluster tree, comparing the current cluster either against all other nodes on the same level or against the sibling nodes to obtain a set of markers per cluster. We subset the tree into its neurons and non-neurons and calculated the global marker genes only versus other cells in the respective subtrees to restrict the marker sets to more relevant genes.
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