methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing.

Motivation: An important downstream analysis following differential expression from RNA sequencing (RNA-Seq) or DNA methylation analysis is the gene set testing to relate significant genes or CpGs to known biological properties. However, the traditional gene set testing approaches result in biased p-values due to the difference in gene length. Existing methods accounting for length bias were primarily developed for RNA-Seq data. For DNA methylation data profiled using the Illumina arrays, separate methods adjusting for the number of CpGs instead of gene length are necessary.

Results: We developed methylGSA, a Bioconductor package for gene set testing in DNA methylation data. Our accompanying Shiny app provides an interactive way of accessing functions and visualizing the results in methylGSA package.

Availability: methylGSA is available at Bioconductor repository: https://bioconductor.org/packages/methylGSA and Shiny app is available at: https://www.ams.sunysb.edu/%7epfkuan/softwares.html#methylGSA.

Supplementary information: Supplementary data are available at Bioinformatics online.