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...

Descripción completa

Detalles Bibliográficos
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
Descripción
Sumario: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.

Ejemplares similares