ChAMP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ChAMP

Tool usage distribution map

This map represents all the scientific publications referring to ChAMP per scientific context
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Associated diseases

This word cloud represents ChAMP usage per disease context

Popular tool citations

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


DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer

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

[…] 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. […]


Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia

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

[…] ea (> 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 known t […]


MethCNA: a database for integrating genomic and epigenomic data in human cancer

BMC Genomics
PMCID: 5810021
PMID: 29433427
DOI: 10.1186/s12864-018-4525-0

[…] were identified by limma package []. Benjamini-Hochberg method was used for p-value adjustment. For detecting copy number alterations from the Illumina 450 k array platform, we employed the R package ChAMP, which infers copy number changes using intensity of individual and surrounding probes []. We used the Beta-value method for differential methylation analysis, since the Beta-value has an intuit […]


The signature of liver cancer in immune cells DNA methylation

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

[…] ples were hybridized and scanned concurrently to mitigate batch effects as recommended by McGill genome center using Illumina Infinum HD technology user guide. Illumina arrays were analyzed using the ChAMP Bioconductor package in R []. IDAT files were used as input in the champ.load function using minfi quality control and normalization options. Raw data were filtered for probes with a detection v […]


Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents

PMCID: 5828554
PMID: 29277323
DOI: 10.1016/j.ebiom.2017.12.018

[…] terogeneity. Principal component analysis (PCA) was used to identify sample outliers in the methylation data. Methylation preprocessing steps were performed using the minfi (), watermelon (), sva (), ChAMP () and FactoMineR () packages of the Bioconductor project operable in R software, version 3.3.0. […]


Effects of maternal obesity on Wharton’s Jelly mesenchymal stromal cells

Sci Rep
PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] essing, and further analyses of the data. The data were normalised to adjust for assay type II bias using the Beta-MIxture Quantile dilation (BMIQ) method from the Chip Analysis Methylation Pipeline (ChAMP) R package. The 450 K array contains 65 single nucleotide polymorphism (SNP) probes that do not interrogate methylation, and these were filtered out. In addition, probes having a detection p-val […]

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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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