(e) } } ) } # Remove metadata for cells not present # 按 cells 保留 meta.data slot(object = x, name = 'meta.data') <- slot(object = x, name = 'meta.data')[cells, , drop = FALSE] # Recalculate nCount and nFeature # 重新计算 nCount 和 nFeature for (assay in Filter...
Change object class testing to use inherits or is.* for R 4.0 compatability Seurat 3.1.1 (2019-09-20) Added New RegroupIdents function to reassign idents based on metadata column majority UpdateSymbolList function to pull new gene names from HGNC Added support for H5AD layers as additional ...
S3method(AddMetaData,Seurat) S3method(Cells,DimReduc) S3method(Cells,default) S3method(Command,Seurat) S3method(DefaultAssay,Assay) S3method(DefaultAssay,DimReduc) S3method(DefaultAssay,Graph) S3method(DefaultAssay,Seurat) S3method(DefaultAssay,SeuratCommand) ...
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called 'knitr' Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart 停止执行 ERROR: lazy loading failed for package 'Seurat' remo...
"CST3")# Subset data.framepbmc<-pbmc[,features]# Add cell ID and identity classespbmc$Cell<- rownames(pbmc)pbmc$Idents<-identity# Use melt to change data.frame formatpbmc<-reshape2::melt(pbmc,id.vars= c("Cell","Idents"),measure.vars=features,variable.name="Feat",value.name="Expr")...
Create Single-Cell Metadata Object for a collection of Seurat Objects. This function creates a metadata object to correspond to a list of single-cell experiments, for storing parent level information. It initializes the object with the experiment and project name, and the creation date. The creat...
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Not an elegant work around, but what I did was create an older version seurat object to run DF, and then exported the metadata of the barcodes and their doublet classification, and then added this data with Seurat::AddMetadata() to a brand new version 5 seurat object, and subset accordi...
xi is 'cell number' of a seurat object, you could get it as 'length(rownames(seur.object@metadata))' , xii is length ofseur.object@active.ident. 'xi != xii ' would cause this kind of error. for a normal 10x scRNAseq experiment, you may name a cell as 'Batch_Sample.barcode', ...