{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T22:39:42Z","timestamp":1772750382084,"version":"3.50.1"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2019,12,6]],"date-time":"2019-12-06T00:00:00Z","timestamp":1575590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01CA224917"],"award-info":[{"award-number":["R01CA224917"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01AA27179"],"award-info":[{"award-number":["R01AA27179"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>DNA methylation can be measured at the single CpG level using sodium bisulfite conversion of genomic DNA followed by sequencing or array hybridization. Many analytic tools have been developed, yet there is still a high demand for a comprehensive and multifaceted tool suite to analyze, annotate, QC and visualize the DNA methylation data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed the CpGtools package to analyze DNA methylation data generated from bisulfite sequencing or Illumina methylation arrays. The CpGtools package consists of three types of modules: (i) \u2018CpG position modules\u2019 focus on analyzing the genomic positions of CpGs, including associating other genomic and epigenomic features to a given list of CpGs and generating the DNA motif logo enriched in the genomic contexts of a given list of CpGs; (ii) \u2018CpG signal modules\u2019 are designed to analyze DNA methylation values, such as performing the PCA or t-SNE analyses, using Bayesian Gaussian mixture modeling to classify CpG sites into fully methylated, partially methylated and unmethylated groups, profiling the average DNA methylation level over user-specified genomics regions and generating the bean\/violin plots and (iii) \u2018differential CpG analysis modules\u2019 focus on identifying differentially methylated CpGs between groups using different statistical methods including Fisher\u2019s Exact Test, Student\u2019s t-test, ANOVA, non-parametric tests, linear regression, logistic regression, beta-binomial regression and Bayesian estimation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CpGtools is written in Python under the open-source GPL license. The source code and documentation are freely available at https:\/\/github.com\/liguowang\/cpgtools.<\/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\/btz916","type":"journal-article","created":{"date-parts":[[2019,12,5]],"date-time":"2019-12-05T04:33:47Z","timestamp":1575520427000},"page":"1598-1599","source":"Crossref","is-referenced-by-count":28,"title":["CpGtools: a python package for DNA methylation analysis"],"prefix":"10.1093","volume":"37","author":[{"given":"Ting","family":"Wei","sequence":"first","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Jinfu","family":"Nie","sequence":"additional","affiliation":[{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology , Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3468-4215","authenticated-orcid":false,"given":"Nicholas B","family":"Larson","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Zhenqing","family":"Ye","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Jeanette E","family":"Eckel-Passow","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Keith D","family":"Robertson","sequence":"additional","affiliation":[{"name":"Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Rochester, MN 55905, USA"}]},{"given":"Jean-Pierre A","family":"Kocher","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2072-4826","authenticated-orcid":false,"given":"Liguo","family":"Wang","sequence":"additional","affiliation":[{"name":"Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic , Rochester, MN 55905, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,12,6]]},"reference":[{"key":"2023051709451407300_btz916-B1","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1037\/a0029146","article-title":"Bayesian estimation supersedes the t test","volume":"142","author":"Kruschke","year":"2013","journal-title":"J. Exp. Psychol. Gen"},{"key":"2023051709451407300_btz916-B2","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat. Biotechnol"},{"key":"2023051709451407300_btz916-B3","first-page":"e141","article-title":"Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates","volume":"43","author":"Wu","year":"2015","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz916\/31605978\/btz916.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/11\/1598\/50361025\/btz916.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/11\/1598\/50361025\/btz916.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T10:26:10Z","timestamp":1684319170000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/11\/1598\/5663456"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,12,6]]},"references-count":3,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2021,7,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz916","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,6,1]]},"published":{"date-parts":[[2019,12,6]]}}}