ChAMP: updated methylation analysis pipeline for Illumina BeadChips

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Abstract

Summary:

The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces.

Availability and implementation:

ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html.

Contact:

a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk

Supplementary information:

Supplementary data are available at Bioinformatics online.

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