{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T18:07:03Z","timestamp":1775844423231,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1054,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: DNA enrichment followed by sequencing is a versatile tool in molecular biology, with a wide variety of applications including genome-wide analysis of epigenetic marks and mechanisms. A common requirement of these diverse applications is a comparison of read coverage between experimental conditions. The amount of samples generated for such comparisons ranges from few replicates to hundreds of samples per condition for epigenome-wide association studies. Consequently, there is an urgent need for software that allows for fast and simple processing and comparison of sequencing data derived from enriched DNA.<\/jats:p>\n               <jats:p>Results: Here, we present a major update of the R\/Bioconductor package MEDIPS, which allows for an arbitrary number of replicates per group and integrates sophisticated statistical methods for the detection of differential coverage between experimental conditions. Our approach can be applied to a diversity of quantitative sequencing data. In addition, our update adds novel functionality to MEDIPS, including correlation analysis between samples, and takes advantage of Bioconductor\u2019s annotation databases to facilitate annotation of specific genomic regions.<\/jats:p>\n               <jats:p>Availability and implementation: The latest version of MEDIPS is available as version 1.12.0 and part of Bioconductor 2.13. The package comes with a manual containing detailed description of its functionality and is available at http:\/\/www.bioconductor.org.<\/jats:p>\n               <jats:p>Contact: \u00a0lienhard@molgen.mpg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt650","type":"journal-article","created":{"date-parts":[[2013,11,14]],"date-time":"2013-11-14T01:41:34Z","timestamp":1384393294000},"page":"284-286","source":"Crossref","is-referenced-by-count":293,"title":["MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments"],"prefix":"10.1093","volume":"30","author":[{"given":"Matthias","family":"Lienhard","sequence":"first","affiliation":[{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}]},{"given":"Christina","family":"Grimm","sequence":"additional","affiliation":[{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"},{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}]},{"given":"Markus","family":"Morkel","sequence":"additional","affiliation":[{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"},{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}]},{"given":"Ralf","family":"Herwig","sequence":"additional","affiliation":[{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}]},{"given":"Lukas","family":"Chavez","sequence":"additional","affiliation":[{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"},{"name":"1 Departments of Vertebrate Genomics and Developmental Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany, 2Department of Rheumatology and Clinical Immunology, 3Institute of Pathology, Laboratory of Molecular Tumour Pathology, Charit\u00e9 Universit\u00e4tsmedizin Berlin, 10117 Berlin, Germany and 4Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,11,13]]},"reference":[{"key":"2023012710391095500_btt650-B1","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1101\/gr.110114.110","article-title":"Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage","volume":"20","author":"Chavez","year":"2010","journal-title":"Genome Res."},{"key":"2023012710391095500_btt650-B2","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1038\/nbt1414","article-title":"A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis","volume":"26","author":"Down","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2023012710391095500_btt650-B3","doi-asserted-by":"crossref","first-page":"e1003250","DOI":"10.1371\/journal.pgen.1003250","article-title":"DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer","volume":"9","author":"Grimm","year":"2013","journal-title":"PLoS Genet."},{"key":"2023012710391095500_btt650-B4","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012710391095500_btt650-B5","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/nature10102","article-title":"Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells","volume":"473","author":"Pastor","year":"2011","journal-title":"Nature"},{"key":"2023012710391095500_btt650-B6","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012710391095500_btt650-B7","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1101\/gr.110601.110","article-title":"Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation","volume":"20","author":"Robinson","year":"2010","journal-title":"Genome Res."},{"key":"2023012710391095500_btt650-B8","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1093\/nar\/gkp992","article-title":"MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome","volume":"38","author":"Serre","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012710391095500_btt650-B9","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1038\/ng1598","article-title":"Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells","volume":"37","author":"Weber","year":"2005","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/2\/284\/48914584\/bioinformatics_30_2_284.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/2\/284\/48914584\/bioinformatics_30_2_284.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T10:45:32Z","timestamp":1674816332000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/2\/284\/223233"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,13]]},"references-count":9,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2014,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt650","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,1,15]]},"published":{"date-parts":[[2013,11,13]]}}}