| Package | Maintainer | Title |
|---|---|---|
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| gaggle | Paul Shannon | Broadcast data between R and Java bioinformatics programs |
| GeneTS | Korbinian Strimmer | Microarray Time Series and Network Analysis |
| graph | Seth Falcon | graph: A package to handle graph data structures |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| hypergraph | Seth Falcon | A package providing hypergraph data structures |
| iSNetwork | Elizabeth Whalen | Interactive Network Plots |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Florian Markowetz | Nested Effects Models to reconstruct phenotypic hierarchies |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| pathRender | Li Long | Render molecular pathways |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| RBGL | Li Long | Interface to boost C++ graph lib |
| Rgraphviz | Jeff Gentry | Provides plotting capabilities for R graph objects |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |