1  Introduction

iSEE is a Bioconductor package designed to produce interactive web applications for the visualisation of biological assays (Figure 2.1).

Figure 1.1: The iSEE app interface, for an example data set.

Initiated in 2017 with single-cell RNA-sequencing in mind, iSEE was designed in such a way that it naturally handles any biological assay that can be stored in a rectangular matrix of features (in rows) and samples (in columns).

What makes iSEE stand out from other interactive web-application is its focus on the SummarizedExperiment class (Figure 1.2), a data structure that is widely used throughout the Bioconductor project, from bulk to single-cell experiments.

Figure 1.2: Schematic representation of the SummarizedExperiment class (reproduced from the vignette of the SummarizedExperiment package).

The well-defined and stable SummarizedExperiment data structure makes it easy for iSEE to automatically detect information commonly stored in dedicated components of SummarizedExperiment objects and display that information in a range of interactive panels, including tables and plots.