Biobase

Biobase is an open-source software package that forms part of the Bioconductor project, designed for biological data analysis using the R programming language. It provides foundational data structures and utilities for handling high-throughput experimental data, such as gene expression measurements from microarrays and sequencing experiments. The package is widely used as infrastructure to support interoperability across Bioconductor tools and workflows.

Central to Biobase are core S4 classes that standardize how experimental data and metadata are stored and accessed. The ExpressionSet class encapsulates a data matrix of observations (for example, expression values) together with phenotypic data describing samples and feature data describing genes or probes, along with experiment-level metadata. Other key classes include AnnotatedDataFrame and MIAME, which facilitate rich annotation of samples and features and documentation of experimental design, respectively. Biobase provides a suite of accessor and manipulation methods, such as exprs, pData, fData, and experimentData, to interact with these structures in a consistent way.

Biobase emphasizes interoperability, enabling downstream Bioconductor packages to read, write, and transform data through a common set of representations. By standardizing data containers and metadata handling, the package supports end-to-end workflows from data import and quality control to normalization and statistical analysis.

The package originated as a foundational component within Bioconductor and is maintained by the Bioconductor community. While Biobase concentrates on data structures and basic utilities, its design supports extension and integration with a broad range of biological datasets and analytical methods, making it a reference point for many Bioconductor analyses.