ChAMP protocols

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

Information


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
Requirements
rmarkdown, knitr
Maintained Yes

Subtool


  • Probe Lasso

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Documentation


Maintainers


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

Publications for ChAMP

ChAMP in pipelines

 (5)
2018
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- […]

2017
PMCID: 5566454
PMID: 28827734
DOI: 10.1038/s41598-017-09335-6

[…] or intact) with individual id as covariate, and defined significance at 5% false-discovery rate (fdr)., methylation was assayed using the illumina 450k beadchip. data were parsed and qced using champ; the probe beta values were quantile-normalized using the ‘dasen’ method from the watermelon package. differential methylation on 425,694 probes post-qc was tested using the cpgassoc package, […]

2016
PMCID: 5053696
PMID: 27056885
DOI: 10.18632/oncotarget.8544

[…] subtraction. data were normalized to background intensity levels and displayed using genome studio software version 2010(ilumina inc.)., the overall different methylation loci were calculated using champ [] and genome studio software version 2010(ilumina inc.). dna methylation profiling data were processed by the champ package. probes with a detection p>0.05 were removed, and β-values […]

2015
PMCID: 4619663
PMID: 26492326
DOI: 10.1371/journal.pgen.1005583

[…] (). to exclude chromosomal abnormalities, we calculated the copy number aberration based on the signal intensities using the method published by feber et al. [] as implemented in the r package champ []. from these results, no abnormalities were found in the samples used ()., multidimensional scaling and clustering was performed based on euclidean distance. for the dna methylation over time […]

2015
PMCID: 4681168
PMID: 26669438
DOI: 10.1186/s13073-015-0246-z

[…] specifically cd3+cd4+ and cd3+cd8+ t lymphocytes, cd19+ b lymphocytes, cd56+ natural killer cells, cd14+ monocytes, and cd15+ granulocytes., we identified dmrs associated with agvhd severity using probe lasso v6.1 []. we applied the following parameters: lassostyle = max, lassoradius = 2000, minsigprobeslasso = 2, mindmrsep = 1000, mindmrsize = 0, and adjpval = 0.1. p values of dmrs […]


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ChAMP in publications

 (44)
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- […]

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 […]

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 […]

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, […]

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 […]


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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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