bioTEA

bioTEA performs differential expression analysis and data preparation for microarray and RNA-seq gene expression datasets from GEO and ArrayExpress (AE), including gene annotation, gene filtering, batch effect correction, sample pairing, and selectable statistical tests.

Key Features:

• Supported data types and sources: Handles microarray and RNA-seq gene expression datasets retrieved from GEO and ArrayExpress (AE).
• Data retrieval and annotation: Supports raw data retrieval, data preparation, and gene annotation.
• Gene-level preprocessing: Provides gene filtering, batch effect correction, and sample pairing options.
• Differential expression analysis: Performs differential expression analysis with user-selectable statistical tests.
• Reproducibility and logging: Saves all user-defined parameters in a single text file and generates detailed log files for each analysis step.
• Implementation and containerization: Integrates R/Bioconductor and Python and is containerized using Docker.

Scientific Applications:

• Transcriptomics differential expression: Identification of differentially expressed genes across conditions in RNA-seq and microarray studies.
• Cross-study and model organism analyses: Comparative analysis and reprocessing of public datasets from GEO and ArrayExpress for studies in model organisms and pathophysiological states.

Methodology:

Computational implementation integrates R/Bioconductor for statistical analysis with Python and is encapsulated within Docker containers.