Biogrid                 Biogrid Network
ChiapetExperimentData-class
                        3CPET used raw data
ChromMaintainers-class
                        Chomatin maintainer networks
CreateCenteredBED-methods
                        Create centered interactions
EnsemblToHGNC           Ensemble to HGNC conversion
EntrezToHGNC            Entrez to HGNC conversion
GOEnrich.folder-methods
                        GO enrichment methods
GenerateNetworks-methods
                        Generate a list of 'igraph' networks
HLDAResult-class        Class '"HLDAResult"'
HPRD                    HPRD protein interaction Network
InferNetworks-methods   Network construction using Hierarchical
                        Dirichlet Process
NetworkCollection-class
                        protein interaction networks maintaining DNA
                        loops
PrepareData-methods     Loading the raw data all at once
R3CPET-package          3CPET: Finding Co-factor Complexes in Chia-PET
                        experiment using a Hierarchical Dirichlet
                        Process
RPKMS                   A gene expression dataset
annotateExpression-methods
                        Add the gene expression attribute to the graph
                        nodes
buildNetworks           Building interaction networks connecting
                        interacting regions
chromosoms              Human chromosom lenghts
cluesOrSota-class       Wrapper for 'clues' and 'sota' S3 classes
clusterInteractions     Grouping DNA interactions by enrichment profile
createIndexes-methods   Preparing TF indexes per region
createServer-methods    Explore results in a web browser
geneLocations           Nucleus located genes
getRegionsInNetwork-methods
                        list of interactions per network
getRegionsIncluster-methods
                        list of interactions per cluster
loadPETs-methods        Parsing ChIA-PET interaction data
loadPPI-methods         Setting the background protein-protein
                        interaction
loadTFBS-methods        Loading TF binding sites
outputGenesPerClusterToDir-methods
                        List of genes in each cluster
outputGenesPerNetworkToDir
                        List of genes controlled by each network
plot3CPETRes-methods    Plotting clustering results
plotTrack-methods       Plot interaction on a genomic track
updateResults-methods   update top maintain networks elements
visualizeCircos-methods
                        Generate circos plot per cluster
visualizeInteractions   Display a Circos plot of ChIA-pet interactions
