ewastools

This tool contains Infinium Human Methylation BeadChip pipeline that can be installed and used inside the Galaxy. The pipeline steps include: raw intensity data loading .idat preprocessing, optional normalisation of the data, quality control with additional sample check. It gives the user the opportunity to perform any of these preparation and data cleaning steps, including the next highly recommended genetic variation annotation step resulting in single nucleotide polymorphism identification and removal by simply running the tool. Finally, the dataset generated through all of these steps can be used to hunt find differentially-methylated positions DMP and regions DMR with respect to a phenotype co-variate.