The clusterProfiler package provides the enrichGO and gseGO functions for ORA and GSEA using GO.16 Instead of providing species-specific GO annotation, clusterProfiler relies on genome-wide annotation packages (OrgDb) released by the Bioconductor project. There are 20 OrgDb packages available in Bioconductor for different species, such as human, mouse, fly, yeast, and worm. These packages are updated biannually. GO annotation for non-model organisms can be queried online via the AnnotationHub package, which provides web services for accessing genome-wide annotations from various data providers (e.g., UCSC, Ensembl, NCBI, STRING, and GENCODE). With the efforts from the Bioconductor community to maintain up-to-date GO annotation for model and non-model organisms, clusterProfiler supports GO analysis on more species compared with other tools. Moreover, a data frame of GO annotation (e.g., retrieve data from the BiomaRt or UniProt database using taxonomic ID) can be used to construct an OrgDb using the AnnotationForge package or directly through the universal interface for enrichment analysis.
