ChAMP: updated methylation analysis pipeline for Illumina BeadChips

Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff, Yuan Tian, Tiffany J Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E Teschendorff

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.

© The Author(s) 2017. Published by Oxford University Press.

Figures

Fig. 1
Fig. 1
The ChAMP pipeline. (A) All functions included in ChAMP. Blue functions used for data preparation. Red functions used to generate analysis results. Yellow functions are GUI functions for visualization. Functions and edges with light green gleam stands for main pipeline (markers are steps for using ChAMP). Dash lines mean functions may not necessarily required. (B) GUI function for visualization of a DMB. The left panel displays parameters for controlling the plot and the table

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Source: PubMed

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