methylGSA

The software tool "methylGSA" addresses a crucial step in downstream analysis following RNA sequencing (RNA-Seq) or DNA methylation analysis, which is gene set testing. Traditional approaches for gene fixed testing often result in biased P-values due to differences in gene length. While existing methods have been developed for RNA-Seq data, DNA methylation data profiled using Illumina arrays requires separate methods that adjust the number of CpGs rather than gene length. The methylGSA package provides a solution for gene set testing in DNA methylation data. The tool accounts for biases related to the number of CpGs. An accompanying Shiny app offers an interactive interface for accessing functions and visualizing results from the methylGSA package.