shinyMethyl: interactive visualization of Illumina 450K methylation arrays

Up to now, more than 10,000 methylation samples from the state-of-the-art 450K microarray have been made available through The Cancer Genome Atlas portal [1] and the Gene Expression Omnibus (GEO) [2]. Large-scale comparison studies, for instance between cancers or tissues, become possible epigenomewidely. These large studies often require a substantial amount of time spent on preprocessing the data and performing quality control. For such studies, it is not rare to encounter significant batch effects, and those can have a dramatic impact on the validity of the biological results [3, 4]. With that in mind, we developed shinyMethyl to make the preprocessing of large 450K datasets intuitive, enjoyable and reproducible. shinyMethyl is an interactive visualization tool for Illumina 450K methylation array data based on the packages minfi and shiny [5, 6].