| Package | Maintainer | Title |
|---|---|---|
| apComplex | Denise Scholtens | Estimate protein complex membership using AP-MS protein data |
| biocGraph | Florian Hahne | Graph examples and use cases in Bioinformatics |
| BioMVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes That Use Biobase |
| BioNet | Marcus Dittrich | Routines for the functional analysis of biological networks |
| CORREP | Dongxiao Zhu | Multivariate Correlation Estimator and Statistical Inference Procedures. |
| DEGraph | Laurent Jacob | Two-sample tests on a graph |
| gaggle | Christopher Bare | Broadcast data between R and Gaggle |
| gene2pathway | Holger Froehlich | Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures |
| GeneAnswers | Gang Feng and Pan Du | Integrated Interpretation of Genes |
| graph | Seth Falcon | graph: A package to handle graph data structures |
| GraphAlignment | Joern P. Meier | GraphAlignment |
| GraphAT | Thomas LaFramboise | Graph Theoretic Association Tests |
| hyperdraw | Paul Murrell | Visualizing Hypergaphs |
| hypergraph | Biocore Team c/o BioC user list | A package providing hypergraph data structures |
| ibh | Kircicegi Korkmaz | Interaction Based Homogeneity for Evaluating Gene Lists |
| KEGGgraph | Jitao David Zhang | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
| keggorthology | VJ Carey | graph support for KO, KEGG Orthology |
| maigesPack | Gustavo H. Esteves | Functions to handle cDNA microarray data, including several methods of data analysis |
| minet | Patrick E. Meyer | Mutual Information NETworks |
| MVCClass | Elizabeth Whalen | Model-View-Controller (MVC) Classes |
| nem | Christian Bender | Nested Effects Models to reconstruct phenotypic hierarchies |
| netresponse | Leo Lahti | NetResponse: functional network analysis |
| ontoTools | Vince Carey | graphs and sparse matrices for working with ontologies; formal objects for nomenclatures with provenance management |
| pathRender | Li Long | Render molecular pathways |
| PCpheno | Nolwenn Le Meur | Phenotypes and cellular organizational units |
| pkgDepTools | Seth Falcon | Package Dependency Tools |
| ppiStats | Tony Chiang | Protein-Protein Interaction Statistical Package |
| qpgraph | Robert Castelo | Reverse engineering of molecular regulatory networks with qp-graphs |
| RBGL | Li Long | An interface to the BOOST graph library |
| RCytoscape | Paul Shannon | Display and manipulate graphs in Cytoscape |
| Rgraphviz | Kasper Hansen | Provides plotting capabilities for R graph objects |
| rHVDM | Martino Barenco | Hidden Variable Dynamic Modeling |
| rsbml | Michael Lawrence | R support for SBML, using libsbml |
| SBMLR | Tomas Radivoyevitch | SBML-R Interface and Analysis Tools |
| ScISI | Tony Chiang | In Silico Interactome |
| simulatorAPMS | Tony Chiang | Computationally simulates the AP-MS technology. |
| SLGI | Nolwenn Le Meur | Synthetic Lethal Genetic Interaction |
| SPIA | Adi Laurentiu Tarca | Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations |
| SQUADD | Martial Sankar | Add-on of the SQUAD Software |