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ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

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.

SUBMITTER: Tian Y

PROVIDER: S-EPMC5860089 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature

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ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

Tian Yuan Y Morris Tiffany J TJ Webster Amy P AP Yang Zhen Z Beck Stephan S Feber Andrew A Teschendorff Andrew E AE

Bioinformatics (Oxford, England) 20171201 24

<h4>Summary</h4>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 ...[more]

PMID: 28961746

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