RDAVIDWebService

RDAVIDWebService provides programmatic access from R to the DAVID (Database for Annotation, Visualization and Integrated Discovery) database for annotation, Gene Ontology analysis, and visualization.

Key Features:

• Class-based interface: Provides a class-based interface for R programs and scripts to access DAVID functionalities.
• Bioconductor distribution: Distributed as an R package through Bioconductor.
• Annotation and visualization: Performs annotation and visualization including Gene Ontology (GO) analysis using GOstats-based direct acyclic graph conversion methods.
• Many-genes-to-many-terms analysis: Supports many-genes-to-many-terms analysis to map sets of genes to multiple annotation terms.
• Automated data retrieval: Supports programmatic upload of gene background lists and retrieval of DAVID-generated reports.
• License: Distributed under the GPL-2 license.

Scientific Applications:

• Gene function analysis: Gene Ontology enrichment and functional interpretation of gene lists.
• Pathway exploration: Pathway annotation and enrichment analysis using DAVID annotations.
• Data integration for systems biology: Integration of gene lists and annotation data to support genomics and systems biology studies.

Methodology:

Class-based R interface to the DAVID web service; GOstats-based direct acyclic graph conversion methods for GO analysis; programmatic upload of gene background lists and retrieval of DAVID reports.