{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T04:00:27Z","timestamp":1776744027238,"version":"3.51.2"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T00:00:00Z","timestamp":1684713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Stichting Cancer Center Amsterdam","award":["CCA2021-9-77"],"award-info":[{"award-number":["CCA2021-9-77"]}]},{"name":"Stichting Cancer Center Amsterdam","award":["CCA2021-5-26"],"award-info":[{"award-number":["CCA2021-5-26"]}]},{"name":"TKI-Health Holland"},{"DOI":"10.13039\/501100003246","name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["VI.Vidi.193.107"],"award-info":[{"award-number":["VI.Vidi.193.107"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and\/or data analysis, can influence the detected RNA expression levels. A critical step, especially in large and low input datasets or studies, is data normalization, which aims at eliminating the variability in data that is not related to biology. Many normalization methods have been developed, each of them relying on different assumptions, making the selection of the appropriate normalization strategy key to preserve biological information. To address this, we developed NormSeq, a free web-server tool to systematically assess the performance of normalization methods in a given dataset. A key feature of NormSeq is the implementation of information gain to guide the selection of the best normalization method, which is crucial to eliminate or at least reduce non-biological variability. Altogether, NormSeq provides an easy-to-use platform to explore different aspects of gene expression data with a special focus on data normalization to help researchers, even without bioinformatics expertise, to obtain reliable biological inference from their data. NormSeq is freely available at: https:\/\/arn.ugr.es\/normSeq.<\/jats:p>","DOI":"10.1093\/nar\/gkad429","type":"journal-article","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T19:33:10Z","timestamp":1684783990000},"page":"W372-W378","source":"Crossref","is-referenced-by-count":9,"title":["NORMSEQ: a tool for evaluation, selection\u00a0and visualization of RNA-Seq normalization methods"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4243-0095","authenticated-orcid":false,"given":"Chantal","family":"Scheepbouwer","sequence":"first","affiliation":[{"name":"Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"},{"name":"Cancer Center Amsterdam, Cancer Biology ,\u00a0 Amsterdam , The Netherlands"},{"name":"Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2248-3114","authenticated-orcid":false,"given":"Michael","family":"Hackenberg","sequence":"additional","affiliation":[{"name":"Genetics Genetics Department, Faculty of Science, Universidad de Granada , Campus de Fuentenueva s\/n , 18071,\u00a0 Granada , Spain"},{"name":"Bioinformatics Laboratory, Biomedical Research Centre (CIBM), Biotechnology Institute , PTS, Avda. del Conocimiento s\/n , 18100\u00a0 Granada , Spain"},{"name":"Excellence Research Unit \u201cModeling Nature\u201d (MNat), University of Granada , Spain"},{"name":"Instituto de Investigaci\u00f3n Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain , Conocimiento s\/n,\u00a018100, Granada , Spain"}]},{"given":"Monique A J","family":"van\u00a0Eijndhoven","sequence":"additional","affiliation":[{"name":"Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"},{"name":"Cancer Center Amsterdam, Imaging and Biomarkers , Amsterdam , The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3909-3606","authenticated-orcid":false,"given":"Alan","family":"Gerber","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"},{"name":"Cancer Center Amsterdam, Cancer Biology ,\u00a0 Amsterdam , The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7357-4406","authenticated-orcid":false,"given":"Michiel","family":"Pegtel","sequence":"additional","affiliation":[{"name":"Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"},{"name":"Cancer Center Amsterdam, Imaging and Biomarkers , Amsterdam , The Netherlands"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0866-4103","authenticated-orcid":false,"given":"Cristina","family":"G\u00f3mez-Mart\u00edn","sequence":"additional","affiliation":[{"name":"Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam , Amsterdam \u00a01081HV, The Netherlands"},{"name":"Cancer Center Amsterdam, Imaging and Biomarkers , Amsterdam , The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2023,5,22]]},"reference":[{"key":"2023070505005948000_B1","doi-asserted-by":"crossref","DOI":"10.1101\/2021.05.04.442244","article-title":"Unbiased and UMI-informed sequencing of cell-free miRNAs at single-nucleotide resolution","author":"Eijndhoven","year":"2021"},{"key":"2023070505005948000_B2","doi-asserted-by":"crossref","first-page":"2630","DOI":"10.1093\/nar\/gky1293","article-title":"Bias-minimized quantification of microRNA reveals widespread alternative processing and 3\u2032 end modification","volume":"47","author":"Kim","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070505005948000_B3","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1101\/gad.350233.122","article-title":"ALL-tRNAseq enables robust tRNA profiling in tissue samples","volume":"37","author":"Scheepbouwer","year":"2023","journal-title":"Genes Dev."},{"key":"2023070505005948000_B4","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","article-title":"RNA sequencing: the teenage years","volume":"20","author":"Stark","year":"2019","journal-title":"Nat. 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