{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,11]],"date-time":"2025-04-11T22:25:34Z","timestamp":1744410334887,"version":"3.37.3"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,3]],"date-time":"2017-11-03T00:00:00Z","timestamp":1509667200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100012118","name":"Ontario Institute for Cancer Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012118","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004376","name":"Terry Fox Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004376","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"CIHR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000109","name":"Prostate Cancer Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000109","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008719","name":"Movember Foundation","doi-asserted-by":"publisher","award":["#RS2014-01"],"award-info":[{"award-number":["#RS2014-01"]}],"id":[{"id":"10.13039\/100008719","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses. To demonstrate its utility, we apply it to a new dataset of 96 genes profiled on 41 prostate tumour and 24 matched normal samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NanoStringNormCNV is implemented in R and is freely available at http:\/\/labs.oicr.on.ca\/boutros-lab\/software\/nanostringnormcnv.<\/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\/btx707","type":"journal-article","created":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T22:23:47Z","timestamp":1509661427000},"page":"1034-1036","source":"Crossref","is-referenced-by-count":3,"title":["NanoStringNormCNV: pre-processing of NanoString CNV data"],"prefix":"10.1093","volume":"34","author":[{"given":"Dorota H","family":"Sendorek","sequence":"first","affiliation":[{"name":"Informatics and Biocomputing Program, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Emilie","family":"Lalonde","sequence":"additional","affiliation":[{"name":"Informatics and Biocomputing Program, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada"},{"name":"Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada"}]},{"given":"Cindy Q","family":"Yao","sequence":"additional","affiliation":[{"name":"Informatics and Biocomputing Program, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Veronica Y","family":"Sabelnykova","sequence":"additional","affiliation":[{"name":"Informatics and Biocomputing Program, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada"}]},{"given":"Robert G","family":"Bristow","sequence":"additional","affiliation":[{"name":"Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada"},{"name":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"}]},{"given":"Paul C","family":"Boutros","sequence":"additional","affiliation":[{"name":"Informatics and Biocomputing Program, Ontario Institute for Cancer Research, University of Toronto, Toronto, ON, Canada"},{"name":"Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada"},{"name":"Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada"}]}],"member":"286","published-online":{"date-parts":[[2017,11,3]]},"reference":[{"key":"2023012712470819300_btx707-B1","doi-asserted-by":"crossref","first-page":"e1004418.","DOI":"10.1371\/journal.pgen.1004418","article-title":"Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats","volume":"10","author":"Brahmachary","year":"2014","journal-title":"PLoS Genet"},{"key":"2023012712470819300_btx707-B2","doi-asserted-by":"crossref","first-page":"479.","DOI":"10.1186\/1471-2105-12-479","article-title":"NanoStriDE: normalization and differential expression analysis of NanoString nCounter data","volume":"12","author":"Brumbaugh","year":"2011","journal-title":"BMC Bioinf"},{"key":"2023012712470819300_btx707-B3","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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