R3CPET-package	R3CPET-package
annotateExpression	annotateExpression-methods
annotateExpression,ChromMaintainers,data.frame-method	annotateExpression-methods
annotateExpression-methods	annotateExpression-methods
betas	HLDAResult-class
betas,HLDAResult-method	HLDAResult-class
betas-methods	HLDAResult-class
Biogrid	Biogrid
buildNetworks	buildNetworks-methods
buildNetworks,ChiapetExperimentData-method	buildNetworks-methods
ChiapetExperimentData	ChiapetExperimentData-class
ChiapetExperimentData-class	ChiapetExperimentData-class
ChromMaintainers	ChromMaintainers-class
ChromMaintainers-class	ChromMaintainers-class
Chromosoms	chromosoms
chromosoms	chromosoms
cluesOrSota-class	cluesOrSota-class
clusterInteractions	clusterInteractions-methods
clusterInteractions,ChromMaintainers-method	clusterInteractions-methods
CreateCenteredBED	CreateCenteredBED-methods
CreateCenteredBED,character-method	CreateCenteredBED-methods
CreateCenteredBED-methods	CreateCenteredBED-methods
createIndexes	createIndexes-methods
createIndexes,ChiapetExperimentData-method	createIndexes-methods
createIndexes-methods	createIndexes-methods
createServer	createServer-methods
createServer,ChiapetExperimentData,NetworkCollection,ChromMaintainers-method	createServer-methods
createServer-methods	createServer-methods
docPerTopic	HLDAResult-class
docPerTopic,HLDAResult-method	HLDAResult-class
docPerTopic-methods	HLDAResult-class
EnsemblToHGNC	EnsemblToHGNC
EntrezToHGNC	EntrezToHGNC
geneLocations	geneLocations
geneLocations.nucleus	geneLocations
GenerateGmlNetworks	ChromMaintainers-class
GenerateGmlNetworks,ChromMaintainers-method	ChromMaintainers-class
GenerateGmlNetworks-methods	ChromMaintainers-class
GenerateNetworks	GenerateNetworks-methods
GenerateNetworks,ChromMaintainers-method	GenerateNetworks-methods
GenerateNetworks-methods	GenerateNetworks-methods
getClusters	ChromMaintainers-class
getClusters,ChromMaintainers-method	ChromMaintainers-class
getClusters-methods	ChromMaintainers-class
getRegionsIncluster	getRegionsIncluster-methods
getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numeric-method	getRegionsIncluster-methods
getRegionsIncluster-methods	getRegionsIncluster-methods
getRegionsInNetwork	getRegionsInNetwork-methods
getRegionsInNetwork,ChromMaintainers,ChiapetExperimentData,numeric-method	getRegionsInNetwork-methods
getRegionsInNetwork-methods	getRegionsInNetwork-methods
GOEnrich.folder	GOEnrich-methods
GOEnrich.folder,character-method	GOEnrich-methods
GOEnrich.folder-methods	GOEnrich-methods
GOEnrich.networks	GOEnrich-methods
GOEnrich.networks,ChromMaintainers-method	GOEnrich-methods
GOEnrich.networks-methods	GOEnrich-methods
HLDAResult	HLDAResult-class
HLDAResult-class	HLDAResult-class
HPRD	HPRD
InferNetworks	InferNetworks-methods
InferNetworks,NetworkCollection-method	InferNetworks-methods
InferNetworks-methods	InferNetworks-methods
loadPETs	loadPETs-methods
loadPETs,ChiapetExperimentData,character-method	loadPETs-methods
loadPETs-methods	loadPETs-methods
loadPPI	loadPPI-methods
loadPPI,ChiapetExperimentData-method	loadPPI-methods
loadPPI-methods	loadPPI-methods
loadTFBS	loadTFBS-methods
loadTFBS,ChiapetExperimentData	loadTFBS-methods
loadTFBS,ChiapetExperimentData,character-method	loadTFBS-methods
loadTFBS-methods	loadTFBS-methods
NetworkCollection	NetworkCollection-class
NetworkCollection-class	NetworkCollection-class
networks	NetworkCollection-class
networks,ChromMaintainers-method	ChromMaintainers-class
networks,NetworkCollection-method	NetworkCollection-class
outputGenesPerClusterToDir	outputGenesPerClusterToDir-methods
outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentData-method	outputGenesPerClusterToDir-methods
outputGenesPerClusterToDir-methods	outputGenesPerClusterToDir-methods
outputGenesPerNetworkToDir	outputGenesPerNetworkToDir-methods
outputGenesPerNetworkToDir,ChromMaintainers,ChiapetExperimentData-method	outputGenesPerNetworkToDir-methods
outputGenesPerNetworkToDir-methods	outputGenesPerNetworkToDir-methods
pet	ChiapetExperimentData-class
pet,ChiapetExperimentData-method	ChiapetExperimentData-class
pet-methods	ChiapetExperimentData-class
pet<-	ChiapetExperimentData-class
pet<-,ChiapetExperimentData-method	ChiapetExperimentData-class
plot3CPETRes	plotRes-methods
plot3CPETRes,ChromMaintainers-method	plotRes-methods
plot3CPETRes-methods	plotRes-methods
plotTrack	plotTrack
plotTrack,ChiapetExperimentData,GRanges-method	plotTrack
plotTrack-methods	plotTrack
ppi	ChiapetExperimentData-class
ppi,ChiapetExperimentData-method	ChiapetExperimentData-class
ppi-methods	ChiapetExperimentData-class
PPI.Biogrid	Biogrid
PPI.HPRD	HPRD
ppi<-	ChiapetExperimentData-class
ppi<-,ChiapetExperimentData-method	ChiapetExperimentData-class
PrepareData	PrepareData-methods
PrepareData,character,character,logical-method	PrepareData-methods
PrepareData-methods	PrepareData-methods
R3CPET	R3CPET-package
RPKMS	RPKMS
sizes	NetworkCollection-class
sizes,NetworkCollection-method	NetworkCollection-class
TF	NetworkCollection-class
TF,NetworkCollection-method	NetworkCollection-class
tfbs	ChiapetExperimentData-class
tfbs,ChiapetExperimentData-method	ChiapetExperimentData-class
tfbs-methods	ChiapetExperimentData-class
tfbs<-	ChiapetExperimentData-class
tfbs<-,ChiapetExperimentData-method	ChiapetExperimentData-class
topEdges	ChromMaintainers-class
topEdges,ChromMaintainers-method	ChromMaintainers-class
topEdges-methods	ChromMaintainers-class
topNodes	ChromMaintainers-class
topNodes,ChromMaintainers-method	ChromMaintainers-class
topNodes-methods	ChromMaintainers-class
updateResults	updateResults-methods
updateResults,ChromMaintainers,NetworkCollection,numeric-method	updateResults-methods
updateResults-methods	updateResults-methods
visualizeCircos	visualizeCircos-methods
visualizeCircos,ChromMaintainers,ChiapetExperimentData,numeric-method	visualizeCircos-methods
visualizeCircos-methods	visualizeCircos-methods
visualizeInteractions	visualizeInteractions-methods
visualizeInteractions,ChiapetExperimentData,GRanges-method	visualizeInteractions-methods
visualizeInteractions-methods	visualizeInteractions-methods
wordsPerTopic	HLDAResult-class
wordsPerTopic,HLDAResult-method	HLDAResult-class
wordsPerTopic-methods	HLDAResult-class
