What is it about?
Genomics data sets are inherently large, diverse, and challenging to explore without advanced programming skills. However, the Bioconductor project has led to the development of data structures carefully designed to facilitate the management of raw and processed data sets, along with information about samples and features present in the data set. Here, we have developed a web-application that automatically detects the available data and metadata stored in the input object and offers users an interface to interactively visualise them with extreme freedom.
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Why is it important?
Most existing software packages provide visualisation methods compatible only with their own internal data representation. The wide adoption of the SummarizedExperiment class throughout packages of the Bioconductor project enables iSEE to inherently support a wide range of genomics technologies (e.g., transcriptomics, proteomics, epigenetics). In addition, the lightweight package and web-based format of the web-application offers various ways to share data with collaborators or the general public.
Perspectives
Writing the software as well as the article was a fantastic and stimulating collaborative experience with co-authors of great skill and character. While it is no secret that the visualisation methods available in iSEE are not fundamentally novel, I believe that our work bringing them all in a single interactive interface opens a world of possibilities for users of all levels of fluency in bioinformatics to dive in and explore genomics data sets in a much more efficient, intuitive, and reproducible way than any other software currently available.
Dr Kevin Christophe Rue-Albrecht
University of Oxford
Read the Original
This page is a summary of: iSEE: Interactive SummarizedExperiment Explorer, F1000Research, June 2018, Faculty of 1000, Ltd.,
DOI: 10.12688/f1000research.14966.1.
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