{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T20:31:57Z","timestamp":1760646717938,"version":"3.37.3"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,10,26]],"date-time":"2017-10-26T00:00:00Z","timestamp":1508976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000097","name":"National Center for Research Resources","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000097","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of \u03b1-diversity and \u03b2-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample\/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https:\/\/acnc-shinyapps.shinyapps.io\/DAME\/. Local installation and source code are available through Github (https:\/\/github.com\/bdpiccolo\/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx686","type":"journal-article","created":{"date-parts":[[2017,10,25]],"date-time":"2017-10-25T19:22:29Z","timestamp":1508959349000},"page":"1050-1052","source":"Crossref","is-referenced-by-count":15,"title":["Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1789-4587","authenticated-orcid":false,"given":"Brian D","family":"Piccolo","sequence":"first","affiliation":[{"name":"Arkansas Children\u2019s Nutrition Center, Little Rock, AR, USA"},{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]},{"given":"Umesh D","family":"Wankhade","sequence":"additional","affiliation":[{"name":"Arkansas Children\u2019s Nutrition Center, Little Rock, AR, USA"},{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]},{"given":"Sree V","family":"Chintapalli","sequence":"additional","affiliation":[{"name":"Arkansas Children\u2019s Nutrition Center, Little Rock, AR, USA"},{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]},{"given":"Sudeepa","family":"Bhattacharyya","sequence":"additional","affiliation":[{"name":"Arkansas Children\u2019s Nutrition Center, Little Rock, AR, USA"},{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]},{"given":"Luo","family":"Chunqiao","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]},{"given":"Kartik","family":"Shankar","sequence":"additional","affiliation":[{"name":"Arkansas Children\u2019s Nutrition Center, Little Rock, AR, USA"},{"name":"Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,10,26]]},"reference":[{"year":"2016","author":"Attali","key":"2023012712474027900_btx686-B1"},{"year":"2016","author":"Barnier","key":"2023012712474027900_btx686-B2"},{"key":"2023012712474027900_btx686-B3","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1093\/bioinformatics\/btu693","article-title":"Seed: a user-friendly tool for exploring and visualizing microbial community data","volume":"31","author":"Beck","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712474027900_btx686-B4","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. 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