repo: An R package for data-centered management of bioinformatic pipelines

Abstract

Background: Reproducibility in Data Analysis research has long been a significant concern, particularly in the areas of Bioinformatics and Computational Biology. Towards the aim of developing reproducible and reusable processes, Data Analysis management tools can help giving structure and coherence to complex data flows. Nonetheless, improved software quality comes at the cost of additional design and planning effort, which may become impractical in rapidly changing development environments. I propose that an adjustment of focus from processes to data in the management of Bioinformatic pipelines may help improving reproducibility with minimal impact on preexisting development practices. Results: In this paper I introduce the repo R package for bioinformatic analysis management. The tool supports a data-centered philosophy that aims at improving analysis reproducibility and reusability with minimal design overhead. The core of repo lies in its support for easy data storage, retrieval, distribution and annotation. In repo the data analysis flow is derived a posteriori from dependency annotations. Conclusions: The repo package constitutes an unobtrusive data and flow management extension of the R statistical language. Its adoption, together with good development practices, can help improving data analysis management, sharing and reproducibility, especially in the fields of Bioinformatics and Computational Biology.