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SeuratExplorer

An R/Shiny app for exploring single-cell RNA-seq data processed in Seurat — no coding required.

SeuratExplorer is a one-command R package that launches an interactive dashboard for the most common single-cell visualizations. It works with a processed Seurat object saved as an .rds or .qs2 file.

• Repo: https://github.com/fentouxungui/SeuratExplorer
• CRAN: https://cran.r-project.org/package=SeuratExplorer
• Live demo: http://netinfo.nibs.ac.cn:666/SeuratExplorer/
• Issues / feature requests: https://github.com/fentouxungui/SeuratExplorer/issues

Why SeuratExplorer

There is no comprehensive tool that lets users without programming skills explore Seurat analysis results. When a bioinformatics analyst hands results to wet-lab users, those users often cannot retrieve or re-plot the data on their own. SeuratExplorer bridges that gap: it wraps command-line Seurat (and related) functions in a point-and-click interface. Users only need R installed (or access to a deployed Shiny Server) and the package.

Key features

• No coding required — interactive point-and-click interface for all analyses.
• Comprehensive visualizations — 10+ plot types.
• Multi-assay support — scRNA-seq, scATAC-seq, spatial, CITE-seq and multi-omics.
• Interactive annotation — rename clusters, define gene-expression-based clusters, combine cluster annotations, compute module scores.
• Publication-ready output — download figures as PDF (WYSIWYG) and tables as CSV.
• Interactivity — results update as you adjust parameters; multiple genes/clusters at once.

Getting started in 30 seconds

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

library(SeuratExplorer)
launchSeuratExplorer()

Then in the browser:

1. Upload your processed Seurat object (.rds / .qs2), or
2. Click Download and Run a demo data to try the app with a bundled demo dataset (see Demo Data).

Wiki pages

• Installation — install from GitHub or CRAN, dependencies, system requirements.
• Quick Start — launch the app and load data.
• Demo Data — the one-click demo dataset: what it is, where it is cached.
• Interface Guide — every menu page and what it does.
• Data Preparation — what your Seurat object needs.
• Launch Options — all launchSeuratExplorer() parameters.
• Troubleshooting & FAQ — common questions and fixes.
• Citation & License.

Companion project

Deploying a multi-user, database-style instance (sample metadata, reports, comments, login) is handled by the companion package SeuratExplorerServer, which builds its UI on top of SeuratExplorer::explorer_server() / explorer_sidebar_ui() / explorer_body_ui().