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```{r} # A list of cell cycle markers, from Tirosh et al, 2015, is loaded with Seurat. We can # segregate this list into markers of G2/M phase and markers of S phase s.genes <- cc.genes$s.genes g2m.genes <- cc.genes$g2m.genes ``` ```{r} #Batch Integration DefaultAssay(seurat_object) = "RNA" seurat_object = FindVariableFeatures(seurat_object) #Select Integration Features integration.features = SelectIntegrationFeatures(SplitObject(seurat_object, split.by = "Batch")) #Remove Cell Cycle Associated Features integration.features2 = integration.features[!integration.features %in% g2m.genes] integration.features2 = integration.features2[!integration.features2 %in% s.genes] #Run FastMNN seurat_object = RunFastMNN(object.list = SplitObject(seurat_object, split.by = "Batch"), features = integration.features2) ```