{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T19:36:16Z","timestamp":1722713776008},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,12,28]],"date-time":"2016-12-28T00:00:00Z","timestamp":1482883200000},"content-version":"vor","delay-in-days":800,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,2,15]]},"abstract":"<jats:p>Summary: In this article we present Simple Exploration of Ecological Data (Seed), a data exploration tool for microbial communities. Seed is written in R using the Shiny library. This provides access to powerful R-based functions and libraries through a simple user interface. Seed allows users to explore ecological datasets using principal coordinate analyses, scatter plots, bar plots, hierarchal clustering and heatmaps.<\/jats:p>\n               <jats:p>Availability and implementation: Seed is open source and available at https:\/\/github.com\/danlbek\/Seed.<\/jats:p>\n               <jats:p>Contact: danlbek@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu693","type":"journal-article","created":{"date-parts":[[2014,10,21]],"date-time":"2014-10-21T03:20:28Z","timestamp":1413861628000},"page":"602-603","source":"Crossref","is-referenced-by-count":7,"title":["Seed: a user-friendly tool for exploring and visualizing microbial community data"],"prefix":"10.1093","volume":"31","author":[{"given":"Daniel","family":"Beck","sequence":"first","affiliation":[{"name":"1Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Dennis","sequence":"additional","affiliation":[{"name":"1Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Foster","sequence":"additional","affiliation":[{"name":"1Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,20]]},"reference":[{"key":"2023020108564130000_btu693-B1","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4419-7976-6","volume-title":"Numerical Ecology with R","author":"Borcard","year":"2011"},{"key":"2023020108564130000_btu693-B2","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":"Nature Methods"},{"key":"2023020108564130000_btu693-B3","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"HMP Consortium et al","year":"2012","journal-title":"Nature"},{"key":"2023020108564130000_btu693-B4","volume-title":"Numerical Ecology","author":"Legendre","year":"2012"},{"key":"2023020108564130000_btu693-B5","doi-asserted-by":"crossref","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":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"2023020108564130000_btu693-B6","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2013"},{"key":"2023020108564130000_btu693-B7","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"Ravel","year":"2011","journal-title":"Proc. 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