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ChAMP | Chip Analysis Methylation Pipeline


Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated analysis pipeline including functions for (i) filtering low quality probes, adjustment for Infinium I and Infinium II probe design, (ii) batch effect correction, detecting differentially methylated positions (DMPs), (iii) finding differentially methylated regions (DMRs) and (iv) detection of copy number aberrations. The software also allows detection of differentially methylated genomic blocks (DMB) and Gene Set Enrichment Analysis (GSEA).

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ChAMP forum

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ChAMP classification

ChAMP specifications

Unique identifier:
Command line interface, Graphical user interface
Biological technology:
Programming languages:
Computer skills:
Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0, GNU General Public License version 2.0
minfi, ChAMPdata, FEM, DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest


  • Probe Lasso

ChAMP distribution


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ChAMP support



  • Andrew Teschendorff <>
  • Stephan Beck <>
  • Tiffany Morris <>
  • Andrew Feber <>


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CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Medical Genomics Group, Paul O’Gorman Building, UCL Cancer Insitute, University College London, London, UK; Cambridge Epigenetix, Jonas Webb Building, Babraham Campus, Cambridge, UK; Statistical Genomics, UCL Cancer Institute, University College London, London, UK; Department of Women’s Cancer, University College London, London, UK

Funding source(s)

Supported by the Royal Society and Chinese Academy of Sciences (Newton Advanced Fellowship 164914), Chinese Scholarship Council (CSC), the MRC (MR/M025411/1) and the UCLH/UCL Comprehensive Biomedical Research Centre and grant NIHR-BTRU-2014-10074 from the National Institute for Health Research (NIHR) Blood & Transplant Research Unit (BTRU).

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