viewseurat

Read-only Shiny app for viewing Seurat objects. Upload an .rds or .qs2 file, or pass a Seurat object directly from R.

Installation

# install.packages("devtools")
devtools::install_github("pcantalupo/viewseurat")

Usage

# View an object directly
ViewSeurat(seurat_obj)

# Launch the upload interface (no object)
ViewSeurat()

You can also open app.R in RStudio and click "Run App" to get the upload interface.

Docker

docker run --rm -p 3838:3838 virushunter/viewseurat

Then open http://localhost:3838 in your browser.

What you can view

• Overview — Visualization of the main elements in a Seurat object with clickable components. The default assay is highlighted.
• Assays — Direct visualization of the counts, data, and scale.data matrices, variable features, and feature metadata in searchable tables.
• Metadata — Per-column summary with distribution graphics, searchable table, and distribution plots.
• Reductions — 2D scatter plots (UMAP, tSNE, PCA, etc.) colored by metadata. Shows which assay was used to build the reduction.
• Images — Spatial tissue plots colored by metadata. Supports 10X Visium and FOV-based platforms (Nanostring CosMx, 10X Xenium).
• The Guts — Raw S4 slot inspection with clickable buttons for all slots

Supported Seurat objects

• Seurat v4 and v5
• SCTAssay (sctransform)
• ChromatinAssay (Signac)
• Spatial- and image-based objects (10X Visium, Xenium, Nanostring CosMx)

This is a viewer only. It does not modify or analyze the Seurat object.