第二步:把seuratv4对象转为seuratv5对象,实现seuratv4对象和v5对象共存:使用seuratv5 读取seurat v4制作的rds文件 代码语言:javascript 复制 pbmc[["RNA5"]]<-as(object=pbmc[["RNA"]],Class="Assay5")DefaultAssay(pbmc)Assays(pbmc)pbmc[["RNA_seuratv4"]]<-pbmc[['RNA']]pbmc[['RNA']]=pbmc[['RNA...
MNN是Haghverdi等人提出的一种批次校正算法,由R语言的batchelor包实现。算法原理及性能评测的细节可参阅2018发表在Nature Biotechnology上的论文:Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. 此算法是Seurat3锚点整合算法的核心部分,也被Monocle3采纳作为批次校正...
Using the exact code from the modulehttps://satijalab.org/seurat/articles/seurat5_integration, Using the exact libraries, but replaced the first steps with the code in the bottom for SCTransform obj <- SCTransform(obj) obj <- RunPCA(obj, npcs= 30, verbose = FALSE) obj <- RunUMAP(obj,...
Unable to write run FastMNN integration after SCTransform in the Seurat 5 Integration vignette#8448 Open Contributor zskylarlimentioned this issueJun 24, 2024 Error in validObject(.Object) : invalid class “LowRankMatrix” object: the supplied seed must support extract_array()#8985 ...