{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T15:35:31Z","timestamp":1774366531128,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,6,14]],"date-time":"2021-06-14T00:00:00Z","timestamp":1623628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018776","name":"University of Florida Health Cancer Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100018776","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 CA155390"],"award-info":[{"award-number":["R01 CA155390"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000774","name":"Defense Threat Reduction Agency","doi-asserted-by":"publisher","award":["HDTRA1-16-1-0048"],"award-info":[{"award-number":["HDTRA1-16-1-0048"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper\u2019s utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit-BGS) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Methylscaper, is implemented in R (version &amp;gt; 4.1) and available on Bioconductor: https:\/\/bioconductor.org\/packages\/methylscaper\/, GitHub: https:\/\/github.com\/rhondabacher\/methylscaper\/, and Web: https:\/\/methylscaper.com.<\/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\/btab438","type":"journal-article","created":{"date-parts":[[2021,6,11]],"date-time":"2021-06-11T15:22:03Z","timestamp":1623424923000},"page":"4857-4859","source":"Crossref","is-referenced-by-count":10,"title":["Methylscaper: an R\/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data"],"prefix":"10.1093","volume":"37","author":[{"given":"Parker","family":"Knight","sequence":"first","affiliation":[{"name":"Department of Biostatistics, University of Florida , Gainesville, FL, USA"}]},{"given":"Marie-Pierre L","family":"Gauthier","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Florida , Gainesville, FL, USA"}]},{"given":"Carolina E","family":"Pardo","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Florida , Gainesville, FL, USA"}]},{"given":"Russell P","family":"Darst","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Florida , Gainesville, FL, USA"}]},{"given":"Kevin","family":"Kapadia","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Florida , Gainesville, FL, USA"}]},{"given":"Hadley","family":"Browder","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Florida , Gainesville, FL, USA"}]},{"given":"Eliza","family":"Morton","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Florida , Gainesville, FL, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9150-8333","authenticated-orcid":false,"given":"Alberto","family":"Riva","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida , Gainesville, FL, USA"}]},{"given":"Michael P","family":"Kladde","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, University of Florida , Gainesville, FL, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5787-476X","authenticated-orcid":false,"given":"Rhonda","family":"Bacher","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Florida , Gainesville, FL, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,6,14]]},"reference":[{"key":"2023051607150575200_btab438-B1","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/s41467-018-03149-4","article-title":"scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells","volume":"9","author":"Clark","year":"2018","journal-title":"Nat. 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