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Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data
The rapid increase in the amount of genomic data provides researchers with an opportunity to integrate diverse datasets and annotations when addressing a wide range of biological questions. However, genomic datasets are deposited on different platforms and are stored in numerous formats from multipl...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041854/ https://www.ncbi.nlm.nih.gov/pubmed/33846313 http://dx.doi.org/10.1038/s41467-021-22381-z |
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author | Cormier, Michael J. Belyeu, Jonathan R. Pedersen, Brent S. Brown, Joseph Köster, Johannes Quinlan, Aaron R. |
author_facet | Cormier, Michael J. Belyeu, Jonathan R. Pedersen, Brent S. Brown, Joseph Köster, Johannes Quinlan, Aaron R. |
author_sort | Cormier, Michael J. |
collection | PubMed |
description | The rapid increase in the amount of genomic data provides researchers with an opportunity to integrate diverse datasets and annotations when addressing a wide range of biological questions. However, genomic datasets are deposited on different platforms and are stored in numerous formats from multiple genome builds, which complicates the task of collecting, annotating, transforming, and integrating data as needed. Here, we developed Go Get Data (GGD) as a fast, reproducible approach to installing standardized data recipes. GGD is available on Github (https://gogetdata.github.io/), is extendable to other data types, and can streamline the complexities typically associated with data integration, saving researchers time and improving research reproducibility. |
format | Online Article Text |
id | pubmed-8041854 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-80418542021-04-30 Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data Cormier, Michael J. Belyeu, Jonathan R. Pedersen, Brent S. Brown, Joseph Köster, Johannes Quinlan, Aaron R. Nat Commun Article The rapid increase in the amount of genomic data provides researchers with an opportunity to integrate diverse datasets and annotations when addressing a wide range of biological questions. However, genomic datasets are deposited on different platforms and are stored in numerous formats from multiple genome builds, which complicates the task of collecting, annotating, transforming, and integrating data as needed. Here, we developed Go Get Data (GGD) as a fast, reproducible approach to installing standardized data recipes. GGD is available on Github (https://gogetdata.github.io/), is extendable to other data types, and can streamline the complexities typically associated with data integration, saving researchers time and improving research reproducibility. Nature Publishing Group UK 2021-04-12 /pmc/articles/PMC8041854/ /pubmed/33846313 http://dx.doi.org/10.1038/s41467-021-22381-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Cormier, Michael J. Belyeu, Jonathan R. Pedersen, Brent S. Brown, Joseph Köster, Johannes Quinlan, Aaron R. Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title | Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title_full | Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title_fullStr | Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title_full_unstemmed | Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title_short | Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data |
title_sort | go get data (ggd) is a framework that facilitates reproducible access to genomic data |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041854/ https://www.ncbi.nlm.nih.gov/pubmed/33846313 http://dx.doi.org/10.1038/s41467-021-22381-z |
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