Learn how to use the iSEE package, in a compact 2-hours workshop!

This is intended as a companion to its big sis workshop package, iUSEiSEE.

This workshop is going to be presented at the EuroBioC2025 conference, taking place in September 2025 in Barcelona, Spain.

Huch, what’s iSEE again?

The iSEE package is a flexible, powerful and extensible application to explore any dataset stored in a SummarizedExperiment object. In turn, any dataset that can be shaped into one or more numerical matrices (“rectangular” datasets) can easily be put into a SummarizedExperiment object. This includes many types of bulk, single-cell, and spatially resolved biological data, as well as many non-biological data types.

iSEE enables a multitude of panels to gain in-depth insight in your data; it does so combining interactivity and reproducibility, and provides an ideal tool for deeper dives into your data.

How to install

To follow this workshop, first install R and RStudio, e.g. following the instructions here. Next, within an R session, the workshop package and all required dependencies can be installed from GitHub as follows:

install.packages("BiocManager")
BiocManager::install("iSEE/iSEEWorkshopEuroBioc2025",
                     dependencies = TRUE,
                     build_vignettes = TRUE)

How to run this workshop

Clone the GitHub repository to a local folder on your computer.
Open the iSEEWorkshopEuroBioc2025.Rproj project file in RStudio.
Navigate to the vignettes folder.
Open the individual R Markdown files and execute their content live!