25-26 November 2026

The iSEE Bioconductor package provides a flexible, powerful and extensible application to explore potentially any omics dataset stored in a SummarizedExperiment object, including single cell and spatially resolved data, but also bulk data (such as transcriptomics and proteomics) and many types of non-biological data. This course provides an extensive introduction to the iSEE package, showcasing the multitude of panels included to gain in-depth insight in the data at hand and generate a comprehensive spectrum of visualizations. Exploring, understanding, and interpreting data with iSEE is achieved also by combining interactivity and reproducibility, making it an ideal companion across all stages of the analysis workflow, also thanks to an ecosystem of packages that extend its functionality (iSEEu, iSEEde, iSEEpathways, iSEEindex, iSEEfier, iSEEtree and more). The course will combine introductory lectures on the iSEE package with practical, hands-on sessions, where participants will be prompted with practical exercises to acquire skills and confidence in the framework.

The course is primarily designed for advanced MSc, PhD and postdoctoral researchers who wish to become proficient in omics data exploration and visualization, with a particular focus on single-cell data.

Most of the examples in this course will center around bulk and single-cell RNA sequencing data. For this reason, a certain background knowledge about these types of data and the questions that are typically addressed with them can be helpful to get the most out of the content.

More precisely, the following pre-requisities are useful:

- Familiarity with bulk or single-cell sequencing data (ideally scRNA-seq).

- Familiarity with the SummarizedExperiment/SingleCellExperiment class, or alternatively the Seurat or AnnData frameworks - basically, any of the widely used ecosystems for working with/storing/processing single-cell data.

- Familiarity with single-cell data visualizations and representations.

By the end of this course, participants will be able to:

- Set up a local environment for running iSEE apps.
- Interact with components of the iSEE user interface to visually inspect and discuss various datasets.
- Identify and locate configurable aspects of iSEE apps.
- Practice interactive visualization over a single-cell RNA-sequencing workflow.
- Imagine use cases and future developments for interactive visualization as part of computational workflows.
- Design and create iSEE instances for collections of datasets.

Daily on-line meetings,  13:00-17:00 CET; offline communication 

Day 1 - Introduction to iSEE and Core Interactive Functionality - 13:00–17:00 CET

Session 1: Preparation - Instructions for installing the required packages and downloading the example data.

Practical: 

Launching the first iSEE application

Session 2: Overview of iSEE - A detailed overview of iSEE and its functionality, from the panel types to the multiple options in each of them.

Practical:
Exploring datasets interactively
Building linked multi-panel visualizations
Interactive exploration exercises

Session 3: Reproducible Workflows in iSEE - Best practices for exploratory workflows

Practical: 
Interactivity and reproducibility in iSEE
Making your exploration reproducible

Day 2 - Cookbook Workflows and Advanced Applications - 13:00–17:00 CET

Session 4: The iSEE cookbook - a set of self-contained recipes with simple-to-advanced tasks one can complete within iSEE.

Practical:
Guided recipe exercises
Independent exploration tasks

Session 5: Applying iSEE to participants’ own projects

Practical:
Troubleshooting and workflow discussion
Additional advanced demonstrations on companion packages, if time permits
Questions and answers

- RNAseq for beginners - ONLINE, 20th-28th of May

 - Introduction to R Shiny - ONLINE, 9-10 June

- Spatial Proteomics in R/Bioconductor- ONLINE, 10-12 November 

- RNA-seq analysis with R/Bioconductor  - ONLINE, 9-18 November

-  Single-cell RNAseq with R/Bioconductor - ONLINE, 16-20 November