执行三种整合方法(CCAIntegration RPCAIntegration HarmonyIntegration) ##整合方法1 combined <- IntegrateLayers( object = combined, method = CCAIntegration, orig.reduction = "pca", new.reduction = "integrated.cca", verbose = FALSE) ##整合方法2 combined <- IntegrateLayers( object = combined, method ...
这里只展示cca和harmony的整合结果 代码语言:javascript 复制 obj<-FindNeighbors(obj,reduction="integrated.cca",dims=1:30)obj<-FindClusters(obj,resolution=2,cluster.name="cca_clusters") obj<-RunUMAP(obj,reduction="integrated.cca",dims=1:30,reduction.name="umap.cca")p1<-DimPlot(obj,reducti...
2.2 Seurat v5 SCT-Normalization Based Integration pacman::p_load(Seurat,SeuratData,dplyr,ggplot2)options(future.globals.maxSize=1e+12){ifnb[["RNA"]]<-split(ifnb[["RNA"]],f=ifnb$stim)ifnb<-ifnb%>%SCTransform(verbose=F)%>%RunPCA(verbose=F)%>%IntegrateLayers(method=CCAIntegration,norm...
(CCA) _ Detailed Seur 33:57 5 DoubletFinder_ Detect doublets in single-cell RNA-Seq data in R _ Detailed wor 24:05 6 Integrate single-cell RNA-Seq data in R using Harmony _ Harmony in Seurat Work 18:09 7 Find markers and cluster identification in single-cell RNA-Seq using Seurat _...
I am comparing Integration methods using the IntegrateLayers() function and am running into an Error when trying to use the scVI method. The other methods (harmony, rpca and cca) I have tried work fine. I am pointing to an anaconda envir...
Hi, I am performing combined analysis of three scRNA-seq samples using Cell Ranger and Seurat. I am trying to understand the purpose of downsampling the matrix/reads with DropletUtils if you are then going to normalize for cell sequencin...