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F1000Res. 2018 Jun 14;7:741. doi: 10.12688/f1000research.14966.1. eCollection 2018.

iSEE: Interactive SummarizedExperiment Explorer.

Author information

1
Kennedy Institute of Rheumatology, University of Oxford, Oxford , OX3 7FY, UK.
2
Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
3
Institute for Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
4
SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, 8057, Switzerland.
5
Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland.
6
Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
#
Contributed equally

Abstract

Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproducibility. We demonstrate the utility and flexibility of iSEE by applying it to explore a range of real transcriptomics and proteomics data sets.

KEYWORDS:

Bioconductor; R; genomics; interactive; proteomics; shiny; transcriptomics; visualization

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