IRFinder-S: a comprehensive suite to discover and explore intron retention

Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification...

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Autores principales: Lorenzi, Claudio, Barriere, Sylvain, Arnold, Katharina, Luco, Reini F., Oldfield, Andrew J., Ritchie, William
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573998/
https://www.ncbi.nlm.nih.gov/pubmed/34749764
http://dx.doi.org/10.1186/s13059-021-02515-8
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author Lorenzi, Claudio
Barriere, Sylvain
Arnold, Katharina
Luco, Reini F.
Oldfield, Andrew J.
Ritchie, William
author_facet Lorenzi, Claudio
Barriere, Sylvain
Arnold, Katharina
Luco, Reini F.
Oldfield, Andrew J.
Ritchie, William
author_sort Lorenzi, Claudio
collection PubMed
description Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02515-8.
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spelling pubmed-85739982021-11-08 IRFinder-S: a comprehensive suite to discover and explore intron retention Lorenzi, Claudio Barriere, Sylvain Arnold, Katharina Luco, Reini F. Oldfield, Andrew J. Ritchie, William Genome Biol Software Accurate quantification and detection of intron retention levels require specialized software. Building on our previous software, we create a suite of tools called IRFinder-S, to analyze and explore intron retention events in multiple samples. Specifically, IRFinder-S allows a better identification of true intron retention events using a convolutional neural network, allows the sharing of intron retention results between labs, integrates a dynamic database to explore and contrast available samples, and provides a tested method to detect differential levels of intron retention. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02515-8. BioMed Central 2021-11-08 /pmc/articles/PMC8573998/ /pubmed/34749764 http://dx.doi.org/10.1186/s13059-021-02515-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://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
Lorenzi, Claudio
Barriere, Sylvain
Arnold, Katharina
Luco, Reini F.
Oldfield, Andrew J.
Ritchie, William
IRFinder-S: a comprehensive suite to discover and explore intron retention
title IRFinder-S: a comprehensive suite to discover and explore intron retention
title_full IRFinder-S: a comprehensive suite to discover and explore intron retention
title_fullStr IRFinder-S: a comprehensive suite to discover and explore intron retention
title_full_unstemmed IRFinder-S: a comprehensive suite to discover and explore intron retention
title_short IRFinder-S: a comprehensive suite to discover and explore intron retention
title_sort irfinder-s: a comprehensive suite to discover and explore intron retention
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8573998/
https://www.ncbi.nlm.nih.gov/pubmed/34749764
http://dx.doi.org/10.1186/s13059-021-02515-8
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