Tag: SingleR

How to use “SingleR” on the marker genes from `FindAllMarkers` for each cluster?

How to use “SingleR” on the marker genes from `FindAllMarkers` for each cluster? 0 Hi, I tried to use SingleR to identify cell types for clusters. I have the table of results from FindAllMakers of Seurat package. I know that I can use: SingleR(GetAssayData(seurat.object, assay = assay, slot = “data”),…

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Can SingleR be reused to identify cell types after subsetting the original Seurat Object

Can SingleR be reused to identify cell types after subsetting the original Seurat Object 0 Hi, I got a Seurat object and applied SingleR to identify cell types. Then subset the epithelial cell then redid the clustering on this cell type only. So now I got some new clusters. My…

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Bioconductor – scRNAseq

DOI: 10.18129/B9.bioc.scRNAseq     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: 3.11 Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso…

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Annotating cell types via integrating a query dataset with a reference dataset and then cluster

  Mostly because it’s typically unnecessary given that reference-based classification should yield a similar result without being subjected to potential biases introduced during the integration process. SingleR (and presumably Seurat, I don’t know as I don’t use it) uses a reference dataset and asks “Which reference sample’s expression profile is…

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