PEGR: a flexible management platform for reproducible epigenomic and genomic research

Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the developme...

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Autores principales: Shao, Danying, Kellogg, Gretta D., Nematbakhsh, Ali, Kuntala, Prashant K., Mahony, Shaun, Pugh, B. Franklin, Lai, William K. M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016988/
https://www.ncbi.nlm.nih.gov/pubmed/35440038
http://dx.doi.org/10.1186/s13059-022-02671-5
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author Shao, Danying
Kellogg, Gretta D.
Nematbakhsh, Ali
Kuntala, Prashant K.
Mahony, Shaun
Pugh, B. Franklin
Lai, William K. M.
author_facet Shao, Danying
Kellogg, Gretta D.
Nematbakhsh, Ali
Kuntala, Prashant K.
Mahony, Shaun
Pugh, B. Franklin
Lai, William K. M.
author_sort Shao, Danying
collection PubMed
description Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02671-5.
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spelling pubmed-90169882022-04-20 PEGR: a flexible management platform for reproducible epigenomic and genomic research Shao, Danying Kellogg, Gretta D. Nematbakhsh, Ali Kuntala, Prashant K. Mahony, Shaun Pugh, B. Franklin Lai, William K. M. Genome Biol Software Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02671-5. BioMed Central 2022-04-19 /pmc/articles/PMC9016988/ /pubmed/35440038 http://dx.doi.org/10.1186/s13059-022-02671-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Shao, Danying
Kellogg, Gretta D.
Nematbakhsh, Ali
Kuntala, Prashant K.
Mahony, Shaun
Pugh, B. Franklin
Lai, William K. M.
PEGR: a flexible management platform for reproducible epigenomic and genomic research
title PEGR: a flexible management platform for reproducible epigenomic and genomic research
title_full PEGR: a flexible management platform for reproducible epigenomic and genomic research
title_fullStr PEGR: a flexible management platform for reproducible epigenomic and genomic research
title_full_unstemmed PEGR: a flexible management platform for reproducible epigenomic and genomic research
title_short PEGR: a flexible management platform for reproducible epigenomic and genomic research
title_sort pegr: a flexible management platform for reproducible epigenomic and genomic research
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9016988/
https://www.ncbi.nlm.nih.gov/pubmed/35440038
http://dx.doi.org/10.1186/s13059-022-02671-5
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