TY - JOUR
T1 - NORMSEQ
T2 - A tool for evaluation, selection and visualization of RNA-Seq normalization methods
AU - Scheepbouwer, Chantal
AU - Hackenberg, Michael
AU - van Eijndhoven, Monique A. J.
AU - Gerber, Alan
AU - Pegtel, Michiel
AU - Gomez-Martin, Cristina
N1 - Funding Information: Stichting Cancer Center Amsterdam [CCA2021-9-77 to C.G., CCA2021-5-26 to A.G.]; TKI-Health Holland [‘AQrate’ project to M.P.]; Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) Talent Programme Vidi [VI.Vidi.193.107 to A.G.]. Funding for open access charge: Stichting Cancer Center Amsterdam [CCA2021-9-77]. Publisher Copyright: © 2023 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2023/7/5
Y1 - 2023/7/5
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85164235707&partnerID=8YFLogxK
U2 - https://doi.org/10.1093/nar/gkad429
DO - https://doi.org/10.1093/nar/gkad429
M3 - Article
C2 - 37216599
SN - 0305-1048
VL - 51
SP - W372-W378
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - W1
ER -