{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T02:36:47Z","timestamp":1776479807250,"version":"3.51.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Helmholtz Foundation"},{"name":"German Network for Bioinformatics"},{"name":"German Ministry of Education and Research","award":["031L0162"],"award-info":[{"award-number":["031L0162"]}]},{"DOI":"10.13039\/501100005972","name":"German Cancer Aid","doi-asserted-by":"publisher","award":["70113869"],"award-info":[{"award-number":["70113869"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010564","name":"Deutsche Zentrum f\u00fcr Lungenforschung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100010564","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["336840530"],"award-info":[{"award-number":["336840530"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union Seventh Framework Program","award":["FP7\/2007\u20132013"],"award-info":[{"award-number":["FP7\/2007\u20132013"]}]},{"name":"European Union Seventh Framework Program","award":["311876"],"award-info":[{"award-number":["311876"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Whole-genome bisulfite sequencing (WGBS) measures DNA methylation at base pair resolution resulting in large bedGraph like coverage files. Current options for processing such files are hindered by discrepancies in file format specification, speed, and memory requirements.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed methrix, an R package, which provides a toolset for systematic analysis of large datasets. Core functionality of the package includes a comprehensive bedGraph or similar tab-separated text file reader\u2014which summarizes methylation calls based on annotated reference indices, infers and collapses strands and handles uncovered reference CpG sites while facilitating a flexible input file format specification. Additional optimized functions for quality control filtering, subsetting and visualization allow user-friendly and effective processing of WGBS results. Easy integration with tools for differentially methylated region (DMR) calling and annotation further eases the analysis of genome-wide methylation data. Overall, methrix enriches established WGBS workflows by bringing together computational efficiency and versatile functionality.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Methrix is implemented as an R package, made available under MIT license at https:\/\/github.com\/CompEpigen\/methrix and can be installed from the Bioconductor repository.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1048","type":"journal-article","created":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T05:04:36Z","timestamp":1607490276000},"page":"5524-5525","source":"Crossref","is-referenced-by-count":13,"title":["Methrix: an R\/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1162-687X","authenticated-orcid":false,"given":"Anand","family":"Mayakonda","sequence":"first","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"},{"name":"Faculty of Biosciences, Heidelberg University , 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9778-9698","authenticated-orcid":false,"given":"Maximilian","family":"Sch\u00f6nung","sequence":"additional","affiliation":[{"name":"Faculty of Biosciences, Heidelberg University , 69117 Heidelberg, Germany"},{"name":"Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) , 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joschka","family":"Hey","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"},{"name":"Faculty of Biosciences, Heidelberg University , 69117 Heidelberg, Germany"},{"name":"German-Israeli Helmholtz Research School in Cancer Biology , partner site Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajbir Nath","family":"Batra","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clarissa","family":"Feuerstein-Akgoz","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"},{"name":"Faculty of Biosciences, Heidelberg University , 69117 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kristin","family":"K\u00f6hler","sequence":"additional","affiliation":[{"name":"Bioinformatics Bachelor Program, Free University Berlin , 14195 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel B","family":"Lipka","sequence":"additional","affiliation":[{"name":"Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) , 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rocio","family":"Sotillo","sequence":"additional","affiliation":[{"name":"Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christoph","family":"Plass","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"},{"name":"German Cancer Research Consortium (DKTK) , partner site Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9383-8555","authenticated-orcid":false,"given":"Pavlo","family":"Lutsik","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reka","family":"Toth","sequence":"additional","affiliation":[{"name":"Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) , 69120 Heidelberg, Germany"},{"name":"Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ) , 69120 Heidelberg, 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