top_genes: Find Top Genes by Cell

In SeuratExplorer: An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'

Find Top Genes by Cell

Description

for each cell, find genes that has high UMI percentage, for example, if a cell has 10000 UMIs, and the UMI percentage cutoff is set to 0.01, then all genes that has more than 10000 * 0.01 = 100 UMIs is thought to be the highly expressed genes for this cell.summary those genes for each cluster, firstly get all highly expressed genes in a cluster, some genes may has less cells, then for each gene, count cells in which this genes is highly expressed, and also calculate the mean and median UMI percentage in those highly expressed cells.

Usage

top_genes(SeuratObj, expr.cut = 0.01, group.by)

Arguments

SeuratObj	Seurat object
expr.cut	UMI percentage cutoff, in a cell, if a gene with UMIs ratio more than this cutoff, this gene will be assigned to highly expressed gene for this cell
group.by	how to group cells

Value

a data frame

SeuratExplorer documentation built on April 4, 2025, 1:57 a.m.