eDAVE – Extension of GDC data analysis, visualization, and exploration tools

Publicly available repositories such as Genomic Data Commons or Gene Expression Omnibus are a valuable research resource useful for hypothesis driven research as well as validation of the results of new experiments. Frequently however, the use of those opulent resources is challenging because advanc...

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Autores principales: Bińkowski, Jan, Taryma-Leśniak, Olga, Sokolowska, Katarzyna Ewa, Przybylowicz, Patrycja Kamila, Staszewski, Melanie, Wojdacz, Tomasz Kazimierz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2023
Materias:
Software/Web Server Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665591/
https://www.ncbi.nlm.nih.gov/pubmed/38022697
http://dx.doi.org/10.1016/j.csbj.2023.10.057
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author Bińkowski, Jan
Taryma-Leśniak, Olga
Sokolowska, Katarzyna Ewa
Przybylowicz, Patrycja Kamila
Staszewski, Melanie
Wojdacz, Tomasz Kazimierz
author_facet Bińkowski, Jan
Taryma-Leśniak, Olga
Sokolowska, Katarzyna Ewa
Przybylowicz, Patrycja Kamila
Staszewski, Melanie
Wojdacz, Tomasz Kazimierz
author_sort Bińkowski, Jan
collection PubMed
description Publicly available repositories such as Genomic Data Commons or Gene Expression Omnibus are a valuable research resource useful for hypothesis driven research as well as validation of the results of new experiments. Frequently however, the use of those opulent resources is challenging because advanced computational skills are required to mine deposited data. To address this challenge, we have developed eDAVE, a user-friendly, web and desktop interface enabling intuitive and robust analysis of almost 12 000 methylomes and transcriptomes from over 200 types of cells and tissues deposited in the Genomic Data Commons repository. The application is implemented in Python, supported for major browsers and available at: https://edave.pum.edu.pl/
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spelling pubmed-106655912023-11-04 eDAVE – Extension of GDC data analysis, visualization, and exploration tools Bińkowski, Jan Taryma-Leśniak, Olga Sokolowska, Katarzyna Ewa Przybylowicz, Patrycja Kamila Staszewski, Melanie Wojdacz, Tomasz Kazimierz Comput Struct Biotechnol J Software/Web Server Article Publicly available repositories such as Genomic Data Commons or Gene Expression Omnibus are a valuable research resource useful for hypothesis driven research as well as validation of the results of new experiments. Frequently however, the use of those opulent resources is challenging because advanced computational skills are required to mine deposited data. To address this challenge, we have developed eDAVE, a user-friendly, web and desktop interface enabling intuitive and robust analysis of almost 12 000 methylomes and transcriptomes from over 200 types of cells and tissues deposited in the Genomic Data Commons repository. The application is implemented in Python, supported for major browsers and available at: https://edave.pum.edu.pl/ Research Network of Computational and Structural Biotechnology 2023-11-04 /pmc/articles/PMC10665591/ /pubmed/38022697 http://dx.doi.org/10.1016/j.csbj.2023.10.057 Text en © 2023 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Software/Web Server Article
Bińkowski, Jan
Taryma-Leśniak, Olga
Sokolowska, Katarzyna Ewa
Przybylowicz, Patrycja Kamila
Staszewski, Melanie
Wojdacz, Tomasz Kazimierz
eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title_full eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title_fullStr eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title_full_unstemmed eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title_short eDAVE – Extension of GDC data analysis, visualization, and exploration tools
title_sort edave – extension of gdc data analysis, visualization, and exploration tools
topic Software/Web Server Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10665591/
https://www.ncbi.nlm.nih.gov/pubmed/38022697
http://dx.doi.org/10.1016/j.csbj.2023.10.057
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