I usually use AddMetaData() to add sample identities or groupings to each of the samples/seurat objects, but I don't know how to do it in an integrated object. I previously integrated samples 1-10 and already processed a lot. I wonder how to a new column "GROUP" that categorizes sam...
Fix in DietSeurat to work with specialized Assay objects Fix p-value return when using the ape implementation of Moran's I Fix bug in FindMarkers when using MAST with a latent variable Updates to Key<-.DimReduc that allow handling of empty reduction column names Allow setting ctrl in CellCy...
第十节:继续以nature文章为例系统阐释降维、聚类等概念,细胞亚群注释三种方法 第十一节:多个样本整合的单细胞数据分析 包括锚定和harmony两种主流的单细胞数据整合算法,同时讲解多线程运算原理和实操。 第十二节:单细胞差异分析 metadata理...
To compute the score, I used the script for 4 known signature genes (of my cell type of interest - labeling "cell_typeA" to trace back) as suggested (#3521). When I use the snippet, it adds on to 4 score (i guess for individual gene) columns appended to metadata viz. cell_typeA...
column_color2=rainbow(length(unique(annot_df_col$month))) names(column_color2)=levels(annot_df_col$month) column_color3=rainbow(length(unique(annot_df_col$Phase))) names(column_color3)=unique(annot_df_col$Phase) anno_col=HeatmapAnnotation(df=annot_df_col,col=list(month=column_color2,Phase...
("https://research.nhgri.nih.gov/", "HydraAEP/download/scriptsdata/", "aepAtlasNonDub.rds") ) ) ## re-order meta.data according to cell order hvulgaris <- orderMetaData( seurat_obj = hvulgaris, seurat_data = hvulgaris@assays$SCT@data ) ## load Hydra vulgaris gene age estimation h...
(Seurat) if(dim(pdata)[2] == 2){ pdata[,"newid"] <- pdata[, id_pdata] } rownames(pdata) <- NULL pdata<-column_to_rownames(pdata, var = id_pdata) pdata<-pdata[rownames(pdata)%in%colnames(eset),] # print(mhead(pdata)) feas<-rownames(eset) feas<-feature_manip...