iSEE: Interactive SummarizedExperiment Explorer

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


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.

Grants and funding

ATLL was supported by core funding from Cancer Research UK [award no. 17197 to JM]. The work of FM is supported by the German Federal Ministry of Education and Research (BMBF 01EO1003).