Create subset of celltypes from scRNA
Hi everyone,
I have an scRNA dataset (10x genomics; "sce.biopsy") from a lymph node biopsy and am particularly interested in B-cells. I have clustered and performed cell type annotation, using Scran/scater/SingleR, by which I detected 19551 B-cells.
library(celldex)
ref <- BlueprintEncodeData()
library(SingleR)
cells <- SingleR(test=sce.biopsy, ref=ref, labels=ref$label.main)
table(cells$labels)
I would like to focus now on differential gene expression in B-cells, not on fibroblasts etc. which are of course also included in the biopsy. Is there a way to create a subset of these B-cells?
Thanks a lot!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Differential Expression Analysis of scRNA seq data with Pseudobulking
written by Sophia •
-
Blog: Novogene Single-cell and Spatial Multi-omics Case Study -Hematological Oncology Research and …
written by Novogene •
-
Facing problem with single cell rna seq annotation using singleR
written by TNF_alpha •
-
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
written by alphaflylizard •
-
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
written by Julia Ma •
-
Single cell analysis of pre- and post treatment
written by Researcher •
-
Error in SingleR when using scRNAseq dataset : number of labels must be equal to number of cells
written by Candice •
-
Annotating UMAP clusters in Seurat with SingleR
written by Aaron •
-
SingleR annotations
written by jyotikataria2008 •
-
How to plot the heat map of a subset of cell types using plotHeatmap from scater package
written by FantasticAI •
You can filter a SingleCellExperiment using the standard
SCE[,ColsToKeep]filtering commands. Since you have a label for every cell you can make a vector of cells to keep. Please be more specific at which step you are struggling.Thanks a lot, this already solved the issue!!