Suerat_SCTransform

library(mixtools)
library(bcellViper)
library (dplyr)
library(Seurat)
library(sctransform)
library(patchwork)

seu<- CreateSeuratObject(counts = counts)
mt.percent <- PercentageFeatureSet(seu, pattern = "^MT-")
seu <- AddMetaData(object=seu,col.name='mt.percent',metadata=mt.percent)

check the quality

pdf("seurat_ht294d_filt.pdf")
seu<-subset(seu, subset=nFeature_RNA>1500 & nCount_RNA<125000 & mt.percent<20 )
VlnPlot(seu, features = c("nFeature_RNA", "nCount_RNA", "mt.percent"), ncol = 3)
VlnPlot(seu, features = c("nFeature_RNA", "nCount_RNA", "mt.percent"),pt.size = 0, ncol = 3)
dev.off()

################ Seurat analysis , parameters:
seu<-SCTransform(object = seu, vars.to.regress = c("nUMI", "mt.percent"))
counts.log<-seu[["SCT"]]@data

lognormailzed

reg<-regul_HT4d_ref_unpr
r1.net<-regul_HT4d_ref_unpr
rank.mat <- RankTransform(counts.log)
r1.pAct <- viper(rank.mat, r1.net, method = 'none')

save(r1.pAct, file="pa_ht294d.rda")