Risa

Risa parses and integrates ISA-Tab formatted experimental metadata into R to enable management, augmentation, and analysis of multi-omics datasets.

Key Features:

• ISA-Tab Format Support: Parses and manipulates ISA-Tab representations of Investigations, Studies, and Assays, including metadata for microarray, flow cytometry, metabolomics (mass spectrometry), and proteomics.
• Integration with R: Converts ISA-Tab datasets into R objects to enable downstream analysis with R packages.
• Data Parsing and Augmentation: Supports parsing ISA-Tab datasets and augmenting them with additional analysis-specific metadata not explicitly present in the original ISA syntax.
• Domain-Specific Interfacing: Interfaces with domain-specific R packages to support tailored workflows for mass spectrometry, microarray, and other experimental data types.
• Package Recommendation: Suggests potentially useful Bioconductor packages for subsequent data processing.
• Metadata Enrichment and Export: Allows saving augmented ISA-Tab files back to disk enriched with analysis-specific metadata generated during R-based workflows.

Scientific Applications:

• Multi-omics integration: Standardizes and combines metadata across multiple experimental techniques to facilitate integrated analyses.
• Reproducible workflows and provenance: Records augmented metadata and analysis-specific annotations to enhance traceability and reproducibility of experimental workflows.
• Mass spectrometry analysis: Supports metadata handling and interfacing for metabolomics (mass spectrometry) datasets.
• DNA microarray analysis: Supports metadata handling and interfacing for microarray datasets.

Methodology:

Parses ISA-Tab formatted datasets into structured R objects, supports metadata augmentation, interfaces with domain-specific R packages, and writes enriched ISA-Tab files to disk.