CELLxGENE 在线平台上面的单细胞转录组数据集整理的非常规范,比如:https://cellxgene.cziscience.com/collections/3f7c572c-cd73-4b51-a313-207c7f20f188 This atlas is an integration of 13 single-cell studies of cells obtained from 8 tumor types and normal tissues, including breast, colorectal, ova...
探究SingleCellExperiment对象——sce ##sce是S4对象,与getGEO返回的对象相似>str(sce,max.level=2)##罗列了所有属性以及下一级菜单的属性>str(sce)Formal class'SingleCellExperiment'[package"SingleCellExperiment"]with9slots ..@int_elementMetadata:Formal class'DFrame'[package"S4Vectors"]with6slots .. .....
CELLxGENE 在线平台上面的单细胞转录组数据集整理的非常规范,比如:https://cellxgene./collections/3f7c572c-cd73-4b51-a313-207c7f20f188 This atlas is an integration of 13 single-cell studies of cells obtained from 8 tumor types and normal tissues, including breast, colorectal, ovary, lung, li...
sce.all<-merge(sceList[[1]],y=sceList[-1],add.cell.ids=samples)as.data.frame(sce.all@assays$RNA@counts[1:10,1:2])head(sce.all@meta.data,10)table(sce.all@meta.data$orig.ident)### step2:QC质控 ### dir.create("./1-QC")setwd("./1-QC")# 如果过滤的太狠,就需要去修改这个...
step11 降维可视化 DimPlot(): DimPlot() / SingleDimPlot() / DefaultDimReduc() / LabelClusters() / FacetTheme()/CenterTitle() //CellSelector()/HoverLocator()/ step12 找差异(标记)基因 FindMarkers(): FindMarkers(): /FindMarkers.Seurat()/FindMarkers.Assay()/FindMarkers.default()/ IdentsTo...
pbmc<-readRDS('G:\\Desktop\\Desktop\\RStudio\\single_cell\\filtered_gene_bc_matrices\\hg19pbmc_tutorial.rds')DefaultAssay(pbmc)<-"RNA"myfilterCommonGenes(input.f=as.matrix(pbmc@assays$RNA@data),output.f=paste0("matrixgenes.gct"),id="GeneSymbol") ...
> sce <- as.SingleCellExperiment(DietSeurat(srat)) > sce class: SingleCellExperiment dim: 36601 8824 metadata(0): assays(2): counts logcounts rownames(36601): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2 rowData names(0): colnames(8824): AAACCCACATGTAACC-1 AAACCCAGTGAGTCAG-1 .....
Demo notebook with basic processing of an example 10x dataset Barcode Formatting Barcodes must be from 10x Genomics exeriments to work with LoupeR. Valid 10x Genomics Single Cell Gene Expression barcodes have the characters ACGT repeated 16 times, followed by an optional GEM well suffix, for ...
Then SCTransform will perform badly as it should be run on a single dataset as a whole instead of the combined dataset. From what I understood what SCTransform does is that it normalizes the dataset as a whole and not on a cell-by-cell basis like the standard NormalizeData would do. ...
Optional name of assay used to generate Graph object See Also dgCMatrix-class SeuratObject Data Structures for Single Cell Data v4.0.1 GPL-3 AuthorsRahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Ho...