iSEE - The interactive SummarizedExperiment Explorer

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The iSEE package provides an interactive user interface for exploring data in objects derived from the SummarizedExperiment class. Particular focus is given to single-cell data stored in the SingleCellExperiment derived class. The user interface is implemented with RStudio's Shiny, with a multi-panel setup for ease of navigation.

This initiative was proposed at the European Bioconductor Meeting in Cambridge, 2017. Current contributors include:

Figure 1. _iSEE_ uses a customisable multi-panel layout.


iSEE can be easily installed from Bioconductor using BiocManager::install():

if (!requireNamespace("BiocManager", quietly = TRUE))
# or also...
BiocManager::install("iSEE", dependencies = TRUE)

Setting dependencies = TRUE should ensure that all packages, including the ones in the Suggests: field of the DESCRIPTION, are installed - this can be essential if you want to reproduce the code in the vignette, for example.


Click to expand the list of features available in iSEE applications.


Sample-level visualization

The iSEE user interface currently contains the following components where each data point represents a single biological sample:

Feature-level visualization

The iSEE user interface currently contains the following components where each data point represents a genomic feature:

Integrated visualization

The iSEE user interface contains the following components that integrate sample and feature information:

Custom panels

The iSEE API allows users to programmatically define their own plotting and table panels. See the section Extending iSEE further below.


Want to try iSEE?

We set up instances of iSEE applications running on diverse types of datasets at those addresses:

Please keep in mind that those public instances are for trial purposes only; yet they demonstrate how you or your system administrator can setup iSEE for analyzing or sharing your precomputed SummarizedExperiment/SingleCellExperiment object.

Extending iSEE

If you want to extend the functionality of iSEE, you can create custom panels which add new possibilities to interact with your data. Custom panels can be defined in independent R packages that include iSEE in the Imports: sections of their DESCRIPTION file. You can find a collection of working examples of how to do it in iSEEu. Feel free to contact the developing team, should you need some clarifications on how iSEE works internally.

Code of Conduct

Please note that the iSEE project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Try the iSEE package in your browser

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iSEE documentation built on Feb. 3, 2021, 2:01 a.m.