Installation

Installation

From GitHub (recommended)

if (!require("devtools")) install.packages("devtools")
devtools::install_github("fentouxungui/SeuratExplorer", dependencies = TRUE)

From CRAN

SeuratExplorer is on CRAN. A few suggested dependencies live outside CRAN, so install them first:

# Bioconductor packages used by optional features
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install(c("ComplexHeatmap", "MAST", "limma", "DESeq2"))

# presto (used for fast marker detection) is GitHub-only
if (!require("devtools")) install.packages("devtools")
devtools::install_github("immunogenomics/presto")

install.packages("SeuratExplorer")

System requirements

• R (>= 4.1.0)
• Seurat (>= 5.4.0)
• SeuratObject (>= 5.3.0)
• ggplot2 (>= 4.0.1)
• curl (used by the one-click demo-data download)

Optional dependencies

These enable specific features and are used conditionally:

Package	Enables
ComplexHeatmap	Cell-level and group-averaged heatmaps
presto	Fast wilcox marker tests in DEG analysis
MAST	test.use = "MAST" in DEG analysis
limma	test.use = "wilcox_limma" / limma-based tests
DESeq2	test.use = "DESeq2" in DEG analysis
Signac	Feature annotations for ATAC assays in Search Features

Verify

library(SeuratExplorer)
packageVersion("SeuratExplorer")