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chevron_left Differential methylation site detection Somatic CNA detection Differentially methylated region detection Raw data import Probe filtering Cell composition correction Batch effect correction Normalization chevron_right

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ChAMP specifications


Unique identifier OMICS_01796
Name ChAMP
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 2.10.2
Stability Stable
rmarkdown, knitr
Maintained Yes


  • Probe Lasso




No version available



  • person_outline Andrew Teschendorff
  • person_outline Stephan Beck
  • person_outline Tiffany Morris
  • person_outline Andrew Feber

Publications for ChAMP

ChAMP citations


Epigenome wide DNA methylation profiling of periprostatic adipose tissue in prostate cancer patients with excess adiposity—a pilot study

Clin Epigenetics
PMCID: 5904983
PMID: 29692867
DOI: 10.1186/s13148-018-0490-3

[…] to the method of benjamin and hochberg’s (bh method) multiple testing procedure []., differentially methylated regions (dmrs) were identified using the “bumphunter” method implemented in the “champ” r package with the parameters (b = 1000, useweights = true, minprobes = 10, pickcutoff = true, and other settings with default values) []., the proportions of significant hyper- […]


A new approach to epigenome wide discovery of non invasive methylation biomarkers for colorectal cancer screening in circulating cell free DNA using pooled samples

Clin Epigenetics
PMCID: 5902929
PMID: 29686738
DOI: 10.1186/s13148-018-0487-y

[…] and correction steps were conducted using the r environment (versions 3.3.3 and 3.4.0) with bioconductor packages. the pipeline was a sequence of r functions adapted from the minfi [] and champ [] bioconductor packages. our dataset was normalized using the functional normalization implemented in the minfi package. this algorithm does not rely on any biological assumption and therefore […]


Altered DNA methylation associated with a translocation linked to major mental illness

NPJ Schizophr
PMCID: 5859082
PMID: 29555928
DOI: 10.1038/s41537-018-0047-7

[…] figure ). multiple testing correction was implemented using the benjamini–hochberg fdr, with a q-value of ≤0.05 deemed to represent genome-wide significance., dmrs were assessed using the champ.lasso() function available in the champ package., probes with an uncorrected p-value of ≤0.05 in the dmp analyses were submitted for dmr analysis. a dmr was defined as a set of at least three […]


DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer

PMCID: 5928889
PMID: 29721079
DOI: 10.7150/thno.23544

[…] by pabinger et al. was used to map the reads from the ion torrent pgm to the reference genome ., all analyses were performed using the statistical software environment r including packages survival, champ, ima, rocr as well as brb array tools for class prediction, and genesis for hierarchical clustering and heatmap visualization., after quantile normalization and type i/ii peak correction, […]


Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia

Clin Epigenetics
PMCID: 5833042
PMID: 29507646
DOI: 10.1186/s13148-018-0463-6

[…] gt; 4 kb from cpg islands) []. arrays were scanned by an illumina hiscan 2000. this methylation data was also used as a validation cohort in []., the resulting idat files were loaded into r using the champ.load function (champ library) [], excluding low quality probes with a detection p value above 0.01 in more than one sample or a beadcount < 3 in at least 5% of samples (n = 1940). probes know […]


The signature of liver cancer in immune cells DNA methylation

Clin Epigenetics
PMCID: 5774119
PMID: 29375724
DOI: 10.1186/s13148-017-0436-1

[…] hcv hepatitis c virus, we delineated differentially methylated cgs between healthy controls and each of the hcc stages independently using the bioconductor package limma [], [] as implemented in champ []. the number of differentially methylated cg sites (p < 1 × 10−7) between each stage of hcc and healthy controls increases with advance in stage; 14,375 for stage 1; 22,018 for stage 2; […]

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ChAMP institution(s)
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
ChAMP 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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