{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T19:45:17Z","timestamp":1740167117897,"version":"3.37.3"},"reference-count":9,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,4,20]],"date-time":"2018-04-20T00:00:00Z","timestamp":1524182400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000092","name":"U.S. National Library of Medicine","doi-asserted-by":"publisher","award":["T15LM007088"],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"In the past few decades, ecologists have developed many diversity indices to describe within and between sample diversity. Consequently, it can be difficult to determine which index to choose and how the distribution of microbial communities affect these indices. We've developed an interactive application, ShinyDiversity<\/ns4:italic>, that dynamically visualizes different alpha or beta diversity indices. In enabling users to select and simultaneously visualize different indices, our application aims to facilitate understanding of how the microbial data affects selected indices.<\/ns4:p>","DOI":"10.12688\/f1000research.14217.1","type":"journal-article","created":{"date-parts":[[2018,4,20]],"date-time":"2018-04-20T10:55:09Z","timestamp":1524221709000},"page":"479","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8724-1872","authenticated-orcid":false,"given":"Eric T.","family":"Leung","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0714-9110","authenticated-orcid":false,"given":"Roshan","family":"Noronha","sequence":"additional","affiliation":[]},{"given":"Ali","family":"Mirza","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7109-4938","authenticated-orcid":false,"given":"Reva","family":"Shenwai","sequence":"additional","affiliation":[]},{"given":"Asterios","family":"Mpatziakas","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2018,4,20]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbw119","article-title":"Measuring the diversity of the human microbiota with targeted next-generation sequencing.","author":"F Finotello","year":"2016","journal-title":"Brief Bioinform."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"W180-W188","DOI":"10.1093\/nar\/gkx295","article-title":"MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data.","volume":"45","author":"A Dhariwal","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"1050-1052","DOI":"10.1093\/bioinformatics\/btx686","article-title":"Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.","volume":"34","author":"B Piccolo","year":"2018","journal-title":"Bioinformatics."},{"article-title":"shiny: Web Application Framework for R","year":"2017","author":"W Chang","key":"ref-4"},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.","volume":"8","author":"P McMurdie","year":"2013","journal-title":"PLoS 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Enzymol."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/7-479\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-479\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/7-479\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,6]],"date-time":"2018-12-06T05:51:34Z","timestamp":1544075494000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/7-479\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,20]]},"references-count":9,"URL":"https:\/\/doi.org\/10.12688\/f1000research.14217.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.15467.r33341","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.15467.r33354","asserted-by":"subject"}]},"ISSN":["2046-1402"],"issn-type":[{"type":"electronic","value":"2046-1402"}],"subject":[],"published":{"date-parts":[[2018,4,20]]},"assertion":[{"value":"Approved with reservations, Approved","URL":"https:\/\/f1000research.com\/articles\/7-479\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.15467.r33354, Jianguo Xia, Institute of Parasitology and Department of Animal Science, McGill University, Montr\u00e9al, QC, Canada, 03 May 2018, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-479\/v1#referee-response-33354","order":0,"name":"referee-response-33354","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.15467.r33341, Richard E. Isaacson, Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA, 16 May 2018, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/7-479\/v1#referee-response-33341","order":1,"name":"referee-response-33341","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Susan Holmes<\/b>; \nPosted: 23 Apr 2018<\/i>; It might be worth noting that this version is very close to Shiny-phyloseq which was published in Bioinformatics https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4287943\/and that entering phyloseq and shiny in google brings you to the page:http:\/\/joey711.github.io\/shiny-phyloseq\/In the academic setting it is often useful to reference previous work and compare new tools to existing ones.","URL":"https:\/\/f1000research.com\/articles\/7-479\/v1#article-response-3609","order":2,"name":"article-response-3609","label":"Article Comment","group":{"name":"article-comments","label":"Article Comments"}},{"value":"Eric Leung was supported by the National Library Of Medicine of the National Institutes of Health under Award Number T15LM007088. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}