Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases

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  • dc.contributor.author Gualdi, Francesco
  • dc.contributor.author Oliva Miguel, Baldomero
  • dc.contributor.author Piñero González, Janet, 1977-
  • dc.date.accessioned 2024-09-16T11:53:58Z
  • dc.date.available 2024-09-16T11:53:58Z
  • dc.date.issued 2024
  • dc.description.abstract Motivation: Integrative Biomedicl Informatics, Research Program on Biomedical Informatics (IBI - GRIB), Hospital Del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF) C/ del Dr. Aiguader 88 Barcelona 08003 Spain.Understanding the genetic basis of complex diseases is one of the main challenges in modern genomics. However, current tools often lack the versatility to efficiently analyze the intricate relationships between genetic variations and disease outcomes. To address this, we introduce Genopyc, a novel Python library designed for comprehensive investigation of how the variants associated to complex diseases affects downstream pathways. Genopyc offers an extensive suite of functions for heterogeneous data mining and visualization, enabling researchers to delve into and integrate biological information from large-scale genomic datasets. Results: In this work, we present the Genopyc library through application to real-world genome wide association studies variants. Using Genopyc to investigate the functional consequences of variants associated to intervertebral disc degeneration enabled a deeper understanding of the potential dysregulated pathways involved in the disease, which can be explored and visualized by exploiting the functionalities featured in the package. Genopyc emerges as a powerful asset for researchers, facilitating the investigation of complex diseases paving the way for more targeted therapeutic interventions. Availability and implementation: Genopyc is available on pip https://pypi.org/project/genopyc/.The source code of Genopyc is available at https://github.com/freh-g/genopyc. A tutorial notebook is available at https://github.com/freh-g/genopyc/blob/main/tutorials/Genopyc_tutorial_notebook.ipynb. Finally, a detailed documentation is available at: https://genopyc.readthedocs.io/en/latest/.
  • dc.description.sponsorship This project was supported by the Marie Sklodowska-Curie International Training Network “disc4all” [#955735]. B.O. acknowledges support from MCIN and the AEI (DOI: 10.13039/501100011033) by grants PID2020-113203RB-I00 and “Unidad de Excelencia María de Maeztu” [ref: CEX2018-000792-M].
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Gualdi F, Oliva B, Piñero J. Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases. Bioinformatics. 2024 Jun 3;40(6):btae379. DOI: 10.1093/bioinformatics/btae379
  • dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btae379
  • dc.identifier.issn 1367-4803
  • dc.identifier.uri http://hdl.handle.net/10230/61100
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Bioinformatics. 2024 Jun 3;40(6):btae379
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/955735
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-113203RB-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
  • dc.rights © The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.other Genètica
  • dc.subject.other Genòmica
  • dc.title Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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Articles (Departament de Medicina i Ciències de la Vida)
Articles (Hospital del Mar Research Institute)
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