clusterProfiler

clusterProfiler performs automated biological-term classification, enrichment analysis, and visualization of gene clusters in an R/Bioconductor framework to interpret quantitative transcriptomics and proteomics data.

Key Features:

• R/Bioconductor package: Implemented as an R package distributed within the Bioconductor ecosystem.
• Automated biological-term classification and enrichment analysis: Automates classification and enrichment workflows for sets of gene clusters.
• GO and KEGG pathway detection: Identifies over-represented Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
• Analysis and visualization modules: Provides integrated analysis and visualization modules within a reusable workflow.
• Supports transcriptomics and proteomics: Processes quantitative data derived from transcriptomics and proteomics studies.
• Species support and extensibility: Includes built-in support for humans, mice, and yeast and is extensible to additional species and ontologies.

Scientific Applications:

• Functional enrichment of gene clusters: Interprets functional profiles associated with clustered gene sets.
• Pathway analysis: Detects biologically relevant pathways via GO and KEGG enrichment.
• Interpretation of omics data: Applies to quantitative transcriptomics and proteomics datasets for functional interpretation.
• Cross-species functional comparisons: Enables comparative analyses across human, mouse, and yeast datasets and can be adapted to other species.

Methodology:

Automates biological-term classification and enrichment analysis to identify over-represented GO terms and KEGG pathways and supplies integrated analysis and visualization modules applied to gene clusters derived from quantitative transcriptomics and proteomics data.