4DNvestigator: time series genomic data analysis toolbox

Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based to...

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Autores principales: Lindsly, Stephen, Chen, Can, Liu, Sijia, Ronquist, Scott, Dilworth, Samuel, Perlman, Michael, Rajapakse, Indika
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2021
Materias:
Heading
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049205/
https://www.ncbi.nlm.nih.gov/pubmed/33794739
http://dx.doi.org/10.1080/19491034.2021.1910437
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author Lindsly, Stephen
Chen, Can
Liu, Sijia
Ronquist, Scott
Dilworth, Samuel
Perlman, Michael
Rajapakse, Indika
author_facet Lindsly, Stephen
Chen, Can
Liu, Sijia
Ronquist, Scott
Dilworth, Samuel
Perlman, Michael
Rajapakse, Indika
author_sort Lindsly, Stephen
collection PubMed
description Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.
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spelling pubmed-80492052021-04-26 4DNvestigator: time series genomic data analysis toolbox Lindsly, Stephen Chen, Can Liu, Sijia Ronquist, Scott Dilworth, Samuel Perlman, Michael Rajapakse, Indika Nucleus Heading Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales. Taylor & Francis 2021-04-02 /pmc/articles/PMC8049205/ /pubmed/33794739 http://dx.doi.org/10.1080/19491034.2021.1910437 Text en © 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Heading
Lindsly, Stephen
Chen, Can
Liu, Sijia
Ronquist, Scott
Dilworth, Samuel
Perlman, Michael
Rajapakse, Indika
4DNvestigator: time series genomic data analysis toolbox
title 4DNvestigator: time series genomic data analysis toolbox
title_full 4DNvestigator: time series genomic data analysis toolbox
title_fullStr 4DNvestigator: time series genomic data analysis toolbox
title_full_unstemmed 4DNvestigator: time series genomic data analysis toolbox
title_short 4DNvestigator: time series genomic data analysis toolbox
title_sort 4dnvestigator: time series genomic data analysis toolbox
topic Heading
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049205/
https://www.ncbi.nlm.nih.gov/pubmed/33794739
http://dx.doi.org/10.1080/19491034.2021.1910437
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