bumphunter

bumphunter is a comprehensive suite of computational tools to analyze DNA methylation (DNAm) data, mainly focusing on data generated by the Infinium HumanMethylation450 array (the '450k' array). While less comprehensive than sequencing-based techniques, this array offers a cost-effective solution for high-throughput DNAm quantification across approximately 450,000 loci, covering a wide range of genomic features. bumphunter is positioned as the go-to software for handling DNAm data due to its incorporation of advanced statistical methods for preprocessing, quality assessment, and the identification of differentially methylated regions across scales from kilobases to megabases.