此教程展示了如何通过基于传统细胞周期相关marker计算细胞周期得分,并在预处理过程中将这些分数从数据中回归,以消除 scRNA-seq 数据中细胞周期异质性的影响。数据:
https://www.dropbox.com/s/3dby3bjsaf5arrw/cell_cycle_vignette_files.zip?dl=1
library(Seurat)
# Read in the expression matrix The first row is a header row, the first column is rownames
exp.mat <- read.table(file = "../data/nestorawa_forcellcycle_expressionMatrix.txt", header = TRUE,
as.is = TRUE, row.names = 1)
# 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
# Create our Seurat object and complete the initalization steps
marrow <- CreateSeuratObject(counts = exp.mat)
marrow <- NormalizeData(marrow)
marrow <- FindVariableFeatures(marrow, selection.method = "vst")
marrow <- ScaleData(mar