seurat_object[[i]] <- RunPCA(seurat_object[[i]], npcs = 50, verbose = FALSE) } # Seurat::ElbowPlot(seurat_object[[1]], ndims = 50) #cluster for (i in seq_along(seurat_object)) { seurat_object[[i]] <- RunUMAP(seurat_object[[i]], reduction = 'pca', dims = 1:20)%>%...
seurat_object[[i]] <- RunUMAP(seurat_object[[i]], reduction = 'pca', dims = 1:20)%>%FindNeighbors(., reduction = 'pca', dims = 1:20)%>%FindClusters(., resolution = 0.4)} 上面就是简单的seurat流程,这是按照seurat V4跑的。安装下最新的DoubletFinder包。看看函数的参数:我们将整个流程...
Erreur : $ operator not defined for this S4 class I am getting the same error, but I am working with Seurat v4 (4.1.0) and would like to stick with it. Which version of Doublet Finder should I use ? Thank you very much!
A better way for the DoubletFinder functions to fetch counts from the object is to use the accessor function Seurat::GetAssayData(). Seurat::GetAssayData(seu, "counts") should work with Seurat v3, v4, v5 since this function is updated with each new release of Seurat. 👍 6 HuangJip...
上面就是简单的seurat流程,这是按照seurat V4跑的。安装下最新的DoubletFinder包。看看函数的参数:我们将整个流程包装在了函数里面: #之前的卸载了,咱们用最新的测试# remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')# library(DoubletFinder) ...