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SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework

BACKGROUND: RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization too...

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Detalles Bibliográficos
Autores principales: Lewinski, Martin, Bramkamp, Yannik, Köster, Tino, Staiger, Dorothee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079501/
https://www.ncbi.nlm.nih.gov/pubmed/32183735
http://dx.doi.org/10.1186/s12859-020-3434-9
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author Lewinski, Martin
Bramkamp, Yannik
Köster, Tino
Staiger, Dorothee
author_facet Lewinski, Martin
Bramkamp, Yannik
Köster, Tino
Staiger, Dorothee
author_sort Lewinski, Martin
collection PubMed
description BACKGROUND: RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators. RESULTS: Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab. CONCLUSION: SEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.
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spelling pubmed-70795012020-03-23 SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework Lewinski, Martin Bramkamp, Yannik Köster, Tino Staiger, Dorothee BMC Bioinformatics Software BACKGROUND: RNA-binding proteins interact with their target RNAs at specific sites. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). Subsequently, the binding sites have to be visualized. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators. RESULTS: Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. This allows, e.g. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Additionally, detailed information on the target genes can be incorporated in another tab. CONCLUSION: SEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing. BioMed Central 2020-03-18 /pmc/articles/PMC7079501/ /pubmed/32183735 http://dx.doi.org/10.1186/s12859-020-3434-9 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Lewinski, Martin
Bramkamp, Yannik
Köster, Tino
Staiger, Dorothee
SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title_full SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title_fullStr SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title_full_unstemmed SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title_short SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
title_sort seqing: web-based visualization of iclip and rna-seq data in an interactive python framework
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079501/
https://www.ncbi.nlm.nih.gov/pubmed/32183735
http://dx.doi.org/10.1186/s12859-020-3434-9
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