1 Introduction

InterCellar is a Bioconductor package that provides an interactive Shiny application to enable the analysis of cell-cell communication from single-cell RNA sequencing (scRNA-seq) data. Every step of the analysis can be performed interactively, thus not requiring any programming skills. Moreover, InterCellar runs on your local machine, avoiding issues related to data privacy.

1.1 Installation

InterCellar is distributed as a Bioconductor package and requires R (version “4.1”) and Bioconductor (version “3.13”).

To install InterCellar package enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


1.2 Launching the app

Once InterCellar is successfully installed, it can be loaded as follow:


In order to start the app, please run the following command:

InterCellar::run_app( reproducible = TRUE )

InterCellar should be opening in a browser. If this does not happen automatically, please open a browser and navigate to the address shown (for example, Listening on The flag reproducible = TRUE ensures that your results will be reproducible across R sessions.

2 Overview of the workflow

The following figure represents InterCellar analysis workflow. We could not miss the opportunity of depicting it as an interstellar journey.