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JarningGau / GeneCooc

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the preparation of input data #1

Open zhoushican opened 9 months ago

zhoushican commented 9 months ago

For the input data seu, up to which step should it be prepared： seu<- scobj %>% NormalizeData() %>% FindVariableFeatures() %>% ScaleData() %>% RunPCA() %>% RunUMAP(dims = 1:10) %>% FindNeighbors() %>% FindClusters(resolution=0.5)

need to remove batch effects from data originating from different samples?

JarningGau commented 9 months ago

GeneCooc is robust to batch effect according to my test.