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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...

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Detalles Bibliográficos
Autores principales: Cormier, Michael J., Belyeu, Jonathan R., Pedersen, Brent S., Brown, Joseph, Köster, Johannes, Quinlan, Aaron R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
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.
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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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