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ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management.

Qian Liu1, Qiang Hu2, Song Liu2

  • 1Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA. Qian.Liu@RoswellPark.org.

BMC Bioinformatics
|January 3, 2024
PubMed
Summary
This summary is machine-generated.

ReUseData is an R software tool that transforms data preprocessing scripts into reproducible data recipes. This enhances genomic data management and reuse for bioinformaticians working with R.

Keywords:
Common Workflow LanguageData managementData reproducibilityData reusabilityGenomic data

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomic Data Science

Background:

  • Genomic data complexity challenges management and reuse.
  • Redundant preprocessing wastes computing resources.
  • Existing tools lack R-specific solutions for versatile data reuse.

Purpose of the Study:

  • Introduce ReUseData, an R package for efficient genomic data management.
  • Provide a versatile and reproducible approach to data management within R.
  • Address the gap in R-specific solutions for data reuse.

Main Methods:

  • Transform ad hoc scripts into Common Workflow Language (CWL)-based data recipes.
  • Standardize and self-contain data recipes for portability.
  • Streamline integration of curated data into downstream analyses.

Main Results:

  • ReUseData enables reproducible generation of curated genomic data files.
  • Data recipes are generic, portable, and reusable across platforms.
  • Facilitates integration with various analysis tools and workflows.

Conclusions:

  • ReUseData offers a reliable, reproducible method for R-based genomic data management.
  • Enhances accessibility and reusability of genomic datasets.
  • Package available on Bioconductor; project website provides more information.