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LOX integrates overall sequence count tallies normalized by total expressed sequence count to provide expression levels for each gene relative to all treatments as well as Bayesian credible intervals.<\/jats:p><jats:p>Availability: \u00a0http:\/\/www.yale.edu\/townsend\/software.html<\/jats:p><jats:p>Contact: \u00a0jeffrey.townsend@yale.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq303","type":"journal-article","created":{"date-parts":[[2010,6,11]],"date-time":"2010-06-11T00:51:37Z","timestamp":1276217497000},"page":"1918-1919","source":"Crossref","is-referenced-by-count":31,"title":["LOX: inferring Level Of eXpression from diverse methods of census sequencing"],"prefix":"10.1093","volume":"26","author":[{"given":"Zhang","family":"Zhang","sequence":"first","affiliation":[{"name":"1 Department of Ecology and Evolutionary Biology and 2Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA"}]},{"given":"Francesc","family":"L\u00f3pez-Gir\u00e1ldez","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolutionary Biology and 2Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA"}]},{"given":"Jeffrey P.","family":"Townsend","sequence":"additional","affiliation":[{"name":"1 Department of Ecology and Evolutionary Biology and 2Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA"},{"name":"1 Department of Ecology and Evolutionary Biology and 2Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,6,10]]},"reference":[{"key":"2023012508013199100_B1","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2009-10-7-r79","article-title":"Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data","volume":"10","author":"Balwierz","year":"2009","journal-title":"Genome Biol."},{"key":"2023012508013199100_B2","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1186\/1471-2164-10-221","article-title":"Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays","volume":"10","author":"Bloom","year":"2009","journal-title":"BMC Genomics"},{"key":"2023012508013199100_B3","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1093\/bib\/bbp019","article-title":"Expression profiling of microRNAs by deep sequencing","volume":"10","author":"Creighton","year":"2009","journal-title":"Brief Bioinform."},{"key":"2023012508013199100_B4","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/oso\/9780198523567.003.0038","article-title":"Efficient Metropolis jumping rules","volume-title":"Bayesian Statistics 5.","author":"Gelman","year":"1996"},{"key":"2023012508013199100_B5","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1016\/j.mimet.2007.09.010","article-title":"Counterselection of prokaryotic ribosomal RNA during reverse transcription using non-random hexameric oligonucleotides","volume":"71","author":"Gonzalez","year":"2007","journal-title":"J. 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