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Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.<\/jats:p>\n               <jats:p>Availability and implementation: ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org<\/jats:p>\n               <jats:p>Contact: \u00a0tiffany.morris@ucl.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt684","type":"journal-article","created":{"date-parts":[[2013,12,14]],"date-time":"2013-12-14T02:19:55Z","timestamp":1386987595000},"page":"428-430","source":"Crossref","is-referenced-by-count":883,"title":["ChAMP: 450k Chip Analysis Methylation Pipeline"],"prefix":"10.1093","volume":"30","author":[{"given":"Tiffany J.","family":"Morris","sequence":"first","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lee M.","family":"Butcher","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Feber","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew E.","family":"Teschendorff","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"},{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur R.","family":"Chakravarthy","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomasz K.","family":"Wojdacz","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Beck","sequence":"additional","affiliation":[{"name":"1 Medical Genomics, and 2Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, 3CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and 4Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,12,12]]},"reference":[{"key":"2023012710410608300_btt684-B1","article-title":"Comprehension Analysis of DNA Methylation Data with RnBeads","author":"Assenov","year":"2013"},{"key":"2023012710410608300_btt684-B2","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.ygeno.2011.07.007","article-title":"High density DNA methylation array with single CpG site resolution","volume":"98","author":"Bibikova","year":"2011","journal-title":"Genomics"},{"key":"2023012710410608300_btt684-B3","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/nrg3273","article-title":"Analysing and interpreting DNA methylation data","volume":"13","author":"Bock","year":"2012","journal-title":"Nat. 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