seurat subset analysis

We hope you will be able to identify them as well and even more subsets on your own, … I have been using Seurat to do analysis of my samples which contain multiple cell types and I would now like to re-run the analysis only on 3 of the clusters, which I have identified as macrophage subtypes. And then I follow the standard Seurat pipeline to do following steps by using the "RNA" assay. The first is to perform differential expression based on pre-annotated anatomical regions within the tissue, which may be determined either from unsupervised clustering or prior knowledge. Seurat part 4 – Cell clustering – NGS Analysis PDF UCell: robust and scalable single-cell gene signature scoring This tutorial demonstrates how to use Seurat (>=3.2) to analyze spatially-resolved RNA-seq data. About Seurat Subset . idents(scrna) 500 & pc1 > 5, idents = "b cells") subset(x = scrna, subset = orig.ident == "replicate1") subset(x = scrna, downsample = 100) subset(x = scrna, features = variablefeatures(object = scrna)) scrna= scrna[,scrna@meta.data$seurat_clusters %in% c(0,2)] scrna= scrna[, idents(scrna) %in% c( "t cell" , "b cell" )] … Correct procedure for subset analysis on integrated data … Subset Seurat [QS6KR9] seurat subset The major features of the Seurat package used to obtain the desired results are FindMarkers, RunPCA, RunUMAP, … Subsetting seurat object to re-analyse specific clusters … This strategy works will in this case, as the clusters above … The data we used is a 10k PBMC data getting from 10x Genomics website.. I subsetted my original object, choosing clusters 1,2 & 4 from both samples to create a new seurat object for each sample which I will merged and re-run … The object serves as a container that contains both data (like the count matrix) and analysis (like PCA, or clustering results) for a single-cell dataset. For a technical discussion of the Seurat object structure, check out our GitHub Wiki. Select genes which we believe are going to be informative. I'm using Seurat to perform a single cell analysis and am interested in exporting the data for all cells within each of my clusters. To use subset on a Seurat object, (see ?subset.Seurat) , you have to provide: ... Differentially expressed genes analysis in Seurat. Ignore any code that parses the function arguments, … We’ve already seen how to load data into a Seurat object and explore sub-populations of cells within a sample, but often we’ll want to compare two samples, such as drug-treated vs. control. SubsetData: Return a subset of the Seurat object Description. Creates a Seurat object containing only a subset of the cells in the original object. Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on. Usage SubsetData(object, ...)

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