DoReMiTra: an R/Bioconductor data package for orchestrating the analysis of radiation transcriptomic studies

Area of Science:

• Molecular Biology
• Bioinformatics
• Radiation Biology

Background:

• Understanding cellular responses to ionizing radiation is crucial for biomedical research and public health.
• Transcriptomics assays, including microarrays and RNA sequencing, are key tools for studying radiation's molecular impact.
• A unified, well-curated collection of radiation transcriptomic datasets has been lacking.

Purpose of the Study:

• To introduce DoReMiTra, the first R/Bioconductor data package consolidating radiation transcriptomics datasets.
• To provide standardized, harmonized metadata and pre-processed data for comparative analyses.
• To facilitate radiation research through a centralized resource and interactive exploration tool.

Main Methods:

• Development of an R/Bioconductor data package named DoReMiTra.
• Integration with Bioconductor's ExperimentHub for data distribution.
• Standardization and harmonization of sample-level metadata.
• Provision of pre-processed SummarizedExperiment objects.
• Development of a Shiny app for interactive visualization.

Main Results:

• DoReMiTra offers a unified collection of radiation transcriptomic datasets.
• The package provides standardized metadata and pre-processed data objects.
• An accompanying Shiny app allows for interactive data exploration.
• The resource is available under the MIT license.

Conclusions:

• DoReMiTra serves as a valuable resource for radiation research.
• It facilitates benchmarking, integrative analyses, and biomarker discovery.
• The package promotes efficient distribution and utilization of radiation transcriptomic data.