| Package | Maintainer | Title |
|---|---|---|
| annaffy | Colin A. Smith | Annotation tools for Affymetrix biological metadata |
| annotate | Biocore Team c/o BioC user list | Annotation for microarrays |
| Category | Biocore Team c/o BioC user list | Category Analysis |
| clusterProfiler | Guangchuang Yu | statistical analysis and visulization of functional profiles for genes and gene clusters |
| domainsignatures | Florian Hahne | Geneset enrichment based on InterPro domain signatures |
| gage | Weijun Luo | Generally Applicable Gene-set Enrichment for Pathway Analysis |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| GlobalAncova | Manuela Hummel | Calculates a global test for differential gene expression between groups |
| globaltest | Jelle Goeman | Testing groups of covariates/features for association with a response variable, with applications to gene set testing |
| GOSemSim | Guangchuang Yu | GO-terms Semantic Similarity Measures |
| joda | Ewa Szczurek | JODA algorithm for quantifying gene deregulation using knowledge |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
| KEGGSOAP | Biocore Team c/o BioC user list | Client-side SOAP access KEGG |
| LiquidAssociation | Yen-Yi Ho | LiquidAssociation |
| miRNApath | James M. Ward | miRNApath: Pathway Enrichment for miRNA Expression Data |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| occugene | Oliver Will | Functions for Multinomial Occupancy Distribution |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |