celltypeEnrich is an R Shiny application for consensus-based annotation of scRNA-seq clusters from marker gene lists. The application uses hypergeometric enrichment analysis against curated cell-type-specific gene sets from 26 reference datasets, including the Human Protein Atlas and Tabula Sapiens, and integrates enrichment results across datasets to produce a consensus cell-type annotation. The application supports marker genes from multiple species through ortholog conversion. A hosted version is available at https://celltypeenrich.gdcb.iastate.edu.
- Clone or download this repository.
- Open the project in R or RStudio.
- Install the required R packages listed below.
- Run shiny_enrich.R to launch the application locally.
Required packages:
library(cowplot)
library(dplyr)
library(ggplot2)
library(htmlwidgets)
library(patchwork)
library(scales)
library(shiny)
library(shinycssloaders)
library(shinyjs)
library(shinythemes)
library(shinyWidgets)
library(stringr)
library(SummarizedExperiment) #this can be installed with Bioconductor
library(tidyr)
library(tidytext)
library(TissueEnrich) #this can be installed with Bioconductor
library(plotly)
A sample marker gene list (Lymphatic Endothelial cells from Litviňuková et al. (https://pubmed.ncbi.nlm.nih.gov/32971526/) is included with the application and can be loaded by selecting ‘Sample List’. This gene list can be used to verify that the application is functioning correctly. When using default parameters, Endothelial is the consensus annotation (A screenshot of the consensus results is below).
TBD