ShinyCell2¶

About¶

ShinyCell2 is an interactive web application for exploring single-cell analysis results. It lets you browse clusters, view marker genes, generate plots, and inspect metadata without writing any code.

Within cell-seek, a ShinyCell2 app is built from a Seurat RDS object using the cell-seek shinycell sub command. With minimal configuration, it validates your inputs, creates the required configuration files, and writes the code needed to deploy an interactive single-cell web app.

You can find more information about ShinyCell2 at its GitHub repository and the OpenOmics fork of ShinyCell2 here.

Who this is for¶

• Building an app? See the cell-seek shinycell command reference for the full list of arguments, examples, and the marker file format.
• Exploring results someone shared with you? See the step-by-step guide for PIs and stakeholders for launching a Shiny App on the NIH Biowulf HPC via HPC OnDemand — no command-line experience required.

What you need¶

In its most basic form, building an app requires only 3 inputs:

• A Seurat RDS object file (with a set of valid cluster identity labels).
• A project title.
• An output directory to write the shiny application files.

You can optionally provide a TSV file with marker genes to add a DEG page to the application.