{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:23:31Z","timestamp":1762899811184,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,9,20]],"date-time":"2019-09-20T00:00:00Z","timestamp":1568937600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Hardiman Scholarship, National University of Ireland Galway"},{"name":"James Hutton Institute, Dundee, Scotland and National University of Ireland Galway"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The overarching aim of microbiome analysis is to uncover the links between microbial phylogeny and function in order to access ecosystem functioning. This can be done using several experimental strategies targeting different biomolecules, including DNA (metagenomics), RNA (metatranscriptomics) and proteins (metaproteomics). Despite the importance of linking microbial function to phylogeny there are currently no visualization tools that effectively integrate this information. Chordomics is a Shiny-based application for linked -omics data analysis, allowing users to visualize microbial function and phylogeny on a single plot and compare datasets across time and environments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Chordomics is available on GitHub: https:\/\/github.com\/kevinmcdonnell6\/chordomics; software is coded in R and JavaScript and a demonstration version is available at https:\/\/kmcd.shinyapps.io\/ChordomicsDemo\/.<\/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\/btz711","type":"journal-article","created":{"date-parts":[[2019,9,16]],"date-time":"2019-09-16T11:53:02Z","timestamp":1568634782000},"page":"1309-1310","source":"Crossref","is-referenced-by-count":3,"title":["Chordomics: a visualization tool for linking function to phylogeny in microbiomes"],"prefix":"10.1093","volume":"36","author":[{"given":"Kevin","family":"McDonnell","sequence":"first","affiliation":[{"name":"Functional Environmental Microbiology, School of Natural Sciences , Ryan Institute, Galway, Ireland"},{"name":"Department of Information Technology, School of Computer Science , National University of Ireland Galway, Galway, Ireland"}]},{"given":"Nicholas","family":"Waters","sequence":"additional","affiliation":[{"name":"Functional Environmental Microbiology, School of Natural Sciences , Ryan Institute, Galway, Ireland"},{"name":"Information and Computational Sciences, James Hutton Institute, Invergowrie , Dundee DD2 5DA, UK"}]},{"given":"Enda","family":"Howley","sequence":"additional","affiliation":[{"name":"Department of Information Technology, School of Computer Science , National University of Ireland Galway, Galway, Ireland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7522-9158","authenticated-orcid":false,"given":"Florence","family":"Abram","sequence":"additional","affiliation":[{"name":"Functional Environmental Microbiology, School of Natural Sciences , Ryan Institute, Galway, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2019,9,20]]},"reference":[{"key":"2023013110135656200_btz711-B1","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D^3 data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. 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