我们使用CellCycleScoring函数计算每个细胞的细胞周期得分,并将计算出的S期和G2/M期的评分保存在metadata中,以及细胞处于G2M,S或G1期的预测分类。通过设置set.ident = TRUE,则CellCycleScoring将Seurat对象中每个细胞的分组信息设置为其所处的细胞周期阶段。 # 使用CellCycleScoring函数计算细胞周期评分 marrow <- Cel...
【CellCycleScoring v5方法概述】 CellCycleScoring v5方法是一种基于细胞染色体DNA含量变化的细胞周期分析技术。该方法通过荧光显微镜观察细胞在不同阶段的DNA含量,从而判断细胞所处的周期阶段。相较于传统方法,CellCycleScoring v5具有更高的灵敏度和准确性,能更好地反映细胞周期的实时动态。 【实验步骤与参数设置】 1...
我们使用CellCycleScoring函数计算每个细胞的细胞周期得分,并将计算出的S期和G2/M期的评分保存在metadata中,以及细胞处于G2M,S或G1期的预测分类。通过设置set.ident = TRUE,则CellCycleScoring将Seurat对象中每个细胞的分组信息设置为其所处的细胞周期阶段。 # 使用CellCycleScoring函数计算细胞周期评分marrow<-CellCycl...
CellCycleScoring算法 clarans算法 CLARANS CLARANS是分割方法中基于随机搜素的大型应用聚类算法,该算法是一种改进的K-MEDOID方法。与以前的k-Medoid算法相比,Clarans更有效。更有效率。实验结果表明,CLARANS能在数千个对象的数据库上高效运行。 它首先随机选择一个点作为当前点,然后随机检查它周围不超过参数Maxneighbor ...
CellCycleScoring报错 运行library(harmony)后代码如下: s.genes <- cc.genes$s.genes g2m.genes <- cc.genes$g2m.genes sce.mergeTEN <- CellCycleScoring(sce.mergeTEN, s.features = s.genes, g2m.features = g2m.genes, set.ident = TRUE)...
#细胞周期s.genes <- cc.genes$s.genesg2m.genes <- cc.genes$g2m.genesTcells <- CellCycleScoring(Tcells, s.features = s.genes, g2m.features = g2m.genes, set.ident = TRUE)#细胞周期信息储存在CellCycleTcells@meta.data$CellCycle <- Idents(Tcells)Idents(Tcells) <- "Lane"#idents函...
Hi Seurat team, I cannot reproduce the same cell cycle scoring in Seurat v5 as the previous versions. I have tried to assign an object using Seurat_4.3.0 which yields 50% of cells in G1 which is what we expected based on experimental dat...
#细胞周期s.genes <- cc.genes$s.genesg2m.genes <- cc.genes$g2m.genesTcells <- CellCycleScoring(Tcells, s.features = s.genes, g2m.features = g2m.genes,set.ident =TRUE)#细胞周期信息储存在CellCycleTcells@meta.data$CellCycle <- Idents(Tcells)...
Cell cycle scoring was performed using CellCycleScoring function. Trajectory analysis was performed using Monocle R package (v 2.18.0). Ordering genes were selected using a cutoff of expression in at least 10 cells and a combination of inter-cluster differential expression and dispersion with a q...
To mitigate the effects of cell cycle heterogeneity on cell clustering, the cell cycle score of each single cell was calculated by using the “CellCycleScoring” function with the cycling orthologous genes in Arabidopsis. These cell cycle effects were then regressed out by the “ScaleData” functi...