{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T23:02:36Z","timestamp":1786575756589,"version":"3.56.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,11,28]],"date-time":"2022-11-28T00:00:00Z","timestamp":1669593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Butler University Holcomb Awards Committee"},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CCSG P30CA016672"],"award-info":[{"award-number":["CCSG P30CA016672"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["UL1TR003167"],"award-info":[{"award-number":["UL1TR003167"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01CA239522"],"award-info":[{"award-number":["U01CA239522"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA251206"],"award-info":[{"award-number":["R01CA251206"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Prostate Cancer SPORE","award":["P50CA140388"],"award-info":[{"award-number":["P50CA140388"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>The NanoTube is an open-source pipeline that simplifies the processing, quality control, normalization and analysis of NanoString nCounter gene expression data. It is implemented in an extensible R library, which performs a variety of gene expression analysis techniques and contains additional functions for integration with other R libraries performing advanced NanoString analysis techniques. Additionally, the NanoTube web application is available as a simple tool for researchers without programming expertise.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The NanoTube R package is available on Bioconductor under the GPL-3 license (https:\/\/www.bioconductor.org\/packages\/NanoTube\/). The R-Shiny application can be downloaded at https:\/\/github.com\/calebclass\/Shiny-NanoTube, or a simplified version of this application can be run on all major browsers, at https:\/\/research.butler.edu\/nanotube\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac762","type":"journal-article","created":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T08:24:28Z","timestamp":1669364668000},"source":"Crossref","is-referenced-by-count":26,"title":["Easy NanoString nCounter data analysis with the NanoTube"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3130-3613","authenticated-orcid":false,"given":"Caleb A","family":"Class","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences, Butler University , Indianapolis, IN 46208, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caiden J","family":"Lukan","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Butler University , Indianapolis, IN 46208, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher A","family":"Bristow","sequence":"additional","affiliation":[{"name":"TRACTION, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim-Anh","family":"Do","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, The University of Texas MD Anderson Cancer Center , Houston, TX 77030, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,28]]},"reference":[{"key":"2023010107513176800_btac762-B2","article-title":"An approach for normalization and quality control for NanoString RNA expression data","volume":"22","author":"Bhattacharya","year":"2020","journal-title":"Brief Bioinformatics"},{"key":"2023010107513176800_btac762-B3","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1093\/bioinformatics\/btz647","article-title":"NACHO: an R package for quality control of NanoString nCounter data","volume":"36","author":"Canouil","year":"2020","journal-title":"Bioinformatics"},{"key":"2023010107513176800_btac762-B4","doi-asserted-by":"crossref","first-page":"e0219566","DOI":"10.1371\/journal.pone.0219566","article-title":"Tumour infiltrating lymphocytes and immune-related genes as predictors of outcome in pancreatic adenocarcinoma","volume":"14","author":"D\u2019Angelo","year":"2019","journal-title":"PLoS One"},{"key":"2023010107513176800_btac762-B5","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nbt1385","article-title":"Direct multiplexed measurement of gene expression with color-coded probe pairs","volume":"26","author":"Geiss","year":"2008","journal-title":"Nat. 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