Bioconductor Task View: GraphsAndNetworks

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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
CORREP Dongxiao Zhu Multivariate Correlation Estimator and Statistical Inference Procedures.
gaggle Dan Tenenbaum Broadcast data between R and other bioinformatics programs
gene2pathway Holger Froehlich Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures
graph Robert Gentleman graph: A package to handle graph data structures
GraphAlignment Joern P. Meier GraphAlignment
GraphAT Thomas LaFramboise Graph Theoretic Association Tests
hypergraph Robert Gentleman A package providing hypergraph data structures
KEGGgraph Jitao David Zhang KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
keggorth 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 Network Inference
MVCClass Elizabeth Whalen Model-View-Controller (MVC) Classes
nem Christian Bender 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
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
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