{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T03:28:56Z","timestamp":1772594936367,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,18]],"date-time":"2020-03-18T00:00:00Z","timestamp":1584489600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Indiana University Precision Health Initiative"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Power analysis is essential to decide the sample size of metagenomic sequencing experiments in a case\u2013control study for identifying differentially abundant (DA) microbes. However, the complexity of microbial data characteristics, such as excessive zeros, over-dispersion, compositionality, intrinsically microbial correlations and variable sequencing depths, makes the power analysis particularly challenging because the analytical form is usually unavailable. Here, we develop a simulation-based power assessment strategy and R package powmic, which considers the complexity of microbial data characteristics. A real data example demonstrates the usage of powmic.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>powmic R package and online tutorial are available at https:\/\/github.com\/lichen-lab\/powmic.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>chen61@iu.edu<\/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\/btaa197","type":"journal-article","created":{"date-parts":[[2020,3,16]],"date-time":"2020-03-16T20:33:59Z","timestamp":1584390839000},"page":"3563-3565","source":"Crossref","is-referenced-by-count":9,"title":["powmic: an R package for power assessment in microbiome case\u2013control studies"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9372-5606","authenticated-orcid":false,"given":"Li","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Medicine"},{"name":"Center for Computational Biology and Bioinformatics , Indiana University School of Medicine, Indianapolis, IN 46202, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,3,18]]},"reference":[{"key":"2023062312020713300_btaa197-B1","author":"Cougoul","year":"2019"},{"key":"2023062312020713300_btaa197-B2","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1080\/03610928808829713","article-title":"Parameter estimation for the dirichlet-multinomial distribution using supplementary beta-binomial data","volume":"17","author":"Danaher","year":"1988","journal-title":"Commun. Stat. Theory Methods"},{"key":"2023062312020713300_btaa197-B3","doi-asserted-by":"crossref","first-page":"3172","DOI":"10.1093\/bioinformatics\/btv349","article-title":"CCLasso: correlation inference for compositional data through Lasso","volume":"31","author":"Fang","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062312020713300_btaa197-B4","doi-asserted-by":"crossref","first-page":"e1002606","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial co-occurrence relationships in the human microbiome","volume":"8","author":"Faust","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023062312020713300_btaa197-B5","doi-asserted-by":"crossref","first-page":"e1002687","DOI":"10.1371\/journal.pcbi.1002687","article-title":"Inferring correlation networks from genomic survey data","volume":"8","author":"Friedman","year":"2012","journal-title":"PLoS Comput. Biol"},{"key":"2023062312020713300_btaa197-B6","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41592-018-0141-9","article-title":"Qiita: rapid, web-enabled microbiome meta-analysis","volume":"15","author":"Gonzalez","year":"2018","journal-title":"Nat. Methods"},{"key":"2023062312020713300_btaa197-B7","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1093\/bioinformatics\/btv183","article-title":"Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA","volume":"31","author":"Kelly","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062312020713300_btaa197-B8","doi-asserted-by":"crossref","first-page":"e1004226","DOI":"10.1371\/journal.pcbi.1004226","article-title":"Sparse and compositionally robust inference of microbial ecological networks","volume":"11","author":"Kurtz","year":"2015","journal-title":"PLoS Comput. Biol"},{"key":"2023062312020713300_btaa197-B9","doi-asserted-by":"crossref","first-page":"e52078","DOI":"10.1371\/journal.pone.0052078","article-title":"Hypothesis testing and power calculations for taxonomic-based human microbiome data","volume":"7","author":"La Rosa","year":"2012","journal-title":"PLoS One"},{"key":"2023062312020713300_btaa197-B10","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12866-018-1154-3","article-title":"A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera","volume":"18","author":"Lappan","year":"2018","journal-title":"BMC Microbiol"},{"key":"2023062312020713300_btaa197-B11","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023062312020713300_btaa197-B12","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1093\/bioinformatics\/btw099","article-title":"A web application for sample size and power calculation in case-control microbiome studies","volume":"32","author":"Mattiello","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062312020713300_btaa197-B13","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation","volume":"40","author":"McCarthy","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023062312020713300_btaa197-B14","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":"2023062312020713300_btaa197-B15","doi-asserted-by":"crossref","first-page":"307","DOI":"10.2307\/1912557","article-title":"Likelihood ratio tests for model selection and non-nested hypotheses","volume":"57","author":"Vuong","year":"1989","journal-title":"Econometrica"},{"key":"2023062312020713300_btaa197-B16","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1208344","article-title":"Linking long-term dietary patterns with gut microbial enterotypes","volume":"334","author":"Wu","year":"2011","journal-title":"Science"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa197\/33151279\/btaa197.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3563\/50670791\/bioinformatics_36_11_3563.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/11\/3563\/50670791\/bioinformatics_36_11_3563.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T12:03:12Z","timestamp":1687521792000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/11\/3563\/5809526"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,3,18]]},"references-count":16,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2020,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa197","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,6]]},"published":{"date-parts":[[2020,3,18]]}}}