{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T11:19:58Z","timestamp":1781522398783,"version":"3.54.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,9,22]],"date-time":"2020-09-22T00:00:00Z","timestamp":1600732800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We developed the MicrobiomeExplorer R package to facilitate the analysis and visualization of microbial communities. The MicrobiomeExplorer R package allows a user to perform typical microbiome analytic workflows and visualize their results, either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows, the application enables automated analysis report generation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Available at https:\/\/github.com\/zoecastillo\/microbiomeExplorer.<\/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\/btaa838","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T19:12:45Z","timestamp":1599851565000},"page":"1317-1318","source":"Crossref","is-referenced-by-count":26,"title":["<i>MicrobiomeExplorer<\/i>: an R package for the analysis and visualization of microbial communities"],"prefix":"10.1093","volume":"37","author":[{"given":"Janina","family":"Reeder","sequence":"first","affiliation":[{"name":"Department of OMNI Bioinformatics, Genentech, Inc , South San Francisco, CA 94080, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mo","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Statistics, The Wharton School, University of Pennsylvania , Philadelphia, PA 19104, USA"},{"name":"Department of Biostatistics, Genentech, Inc , South San Francisco, CA 94080, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua S","family":"Kaminker","sequence":"additional","affiliation":[{"name":"Department of OMNI Bioinformatics, Genentech, Inc , South San Francisco, CA 94080, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8221-7139","authenticated-orcid":false,"given":"Joseph N","family":"Paulson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Genentech, Inc , South San Francisco, CA 94080, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,30]]},"reference":[{"key":"2023051706053889900_btaa838-B1","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s40168-017-0235-0","article-title":"Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens","volume":"5","author":"Chopyk","year":"2017","journal-title":"Microbiome"},{"key":"2023051706053889900_btaa838-B2","author":"McMurdie","year":"2016"},{"key":"2023051706053889900_btaa838-B3","first-page":"719","author":"Oksanen","year":"2007"},{"key":"2023051706053889900_btaa838-B4","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/nmeth.2658","article-title":"Differential abundance analysis for microbial marker-gene surveys","volume":"10","author":"Paulson","year":"2013","journal-title":"Nat. Methods"},{"key":"2023051706053889900_btaa838-B5","doi-asserted-by":"crossref","DOI":"10.1201\/9780429447273","volume-title":"Interactive Web-Based Data Visualization with R, Plotly, and Shiny","author":"Sievert","year":"2020"},{"key":"2023051706053889900_btaa838-B6","doi-asserted-by":"crossref","first-page":"2777","DOI":"10.1093\/nar\/gky136","article-title":"Metaviz: interactive statistical and visual analysis of metagenomic data","volume":"46","author":"Wagner","year":"2018","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\/btaa838\/34055912\/btaa838.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1317\/50359511\/btaa838.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/9\/1317\/50359511\/btaa838.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T06:11:15Z","timestamp":1684303875000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/9\/1317\/5909986"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,10,30]]},"references-count":6,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2021,6,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa838","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,5,1]]},"published":{"date-parts":[[2020,10,30]]}}}