R3CPET
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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Functions
192
Source code
17
Man pages
35
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R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
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API for R3CPET
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Global functions
.ConvertToHDA Source code
.DavidGOAnalysis Source code
.DavidGOAnalysis.folder Source code
.DoDAVIDGOAnnotation Source code
.DoDAVIDGOAnnotation.list Source code
.GetClusterInfo Source code
.ReadPET Source code
.ReadTFBS Source code
.RemoveOutliers Source code
.annotateNodesExpression Source code
.bracketedStrings Source code
.build.PETNetworks.byedge Source code
.buildNetFromEdges Source code
.calculate.all.shortest.paths Source code
.check.pet Source code
.check.tfbs Source code
.checkChIAPETFormat Source code
.create.datatables_chip Source code
.createBEDFile.Centered Source code
.edgeMaker Source code
.filter.singnifTF Source code
.filterByExpression Source code
.filterPPI Source code
.formatDAVIDResult Source code
.get.ClusterInvolvedGenes Source code
.get.NetworksGenes Source code
.get.TFSpace Source code
.get.TFsStat Source code
.get.network.byedge Source code
.getNodesList Source code
.getNuclearPPI Source code
.plot.TopicsSimilarity Source code
.plot.clustOrderHeatmap Source code
.plot.sota Source code
.plotAllNet Source code
.plotNetwork Source code
.preparareData Source code
.print.topwords Source code
.valid.ChromMaintainers Source code
.valid.HLDAResult Source code
.valid.NetworkCollection Source code
.valid.NetworkCollection.TFCollection Source code
.valid.NetworkCollection.networks Source code
.valid.NetworkCollection.sizes Source code
.valid.buildNetworks Source code
Biogrid Man page
ChiapetExperimentData Man page Source code
ChiapetExperimentData-class Man page
ChromMaintainers Man page Source code
ChromMaintainers-class Man page
Chromosoms Man page
ConvertGeneNameToHGNC Source code
CreateCenteredBED Man page
CreateCenteredBED,character-method Man page
CreateCenteredBED-methods Man page
EnsemblToHGNC Man page Source code
EntrezToHGNC Man page Source code
GOEnrich.folder Man page
GOEnrich.folder,character-method Man page
GOEnrich.folder-methods Man page
GOEnrich.networks Man page
GOEnrich.networks,ChromMaintainers-method Man page
GOEnrich.networks-methods Man page
GenerateGmlNetworks Man page
GenerateGmlNetworks,ChromMaintainers-method Man page
GenerateGmlNetworks-methods Man page
GenerateNetworks Man page
GenerateNetworks,ChromMaintainers-method Man page
GenerateNetworks-methods Man page
HLDAResult Man page Source code
HLDAResult-class Man page
HPRD Man page
InferNetworks Man page
InferNetworks,NetworkCollection-method Man page
InferNetworks-methods Man page
NetworkCollection Man page Source code
NetworkCollection-class Man page
PPI.Biogrid Man page
PPI.HPRD Man page
PrepareData Man page
PrepareData,character,character,logical-method Man page
PrepareData-methods Man page
R3CPET Man page
R3CPET-package Man page
RPKMS Man page
RunHLDA Source code
TF Man page
TF,NetworkCollection-method Man page
annotateExpression Man page
annotateExpression,ChromMaintainers,data.frame-method Man page Man page
annotateExpression-methods Man page
betas Man page
betas,HLDAResult-method Man page
betas-methods Man page
buildNetworks Man page
buildNetworks,ChiapetExperimentData-method Man page
chromosoms Man page
cluesOrSota-class Man page
cluster,ChromMaintainers-method Man page
clusterInteractions Man page
clusterInteractions,ChromMaintainers-method Man page
createIndexes Man page
createIndexes,ChiapetExperimentData-method Man page
createIndexes-methods Man page
createServer Man page
createServer,ChiapetExperimentData,NetworkCollection,ChromMainta Man page
createServer-methods Man page
docPerTopic Man page
docPerTopic,HLDAResult-method Man page
docPerTopic-methods Man page
geneLocations Man page
geneLocations.nucleus Man page
getClusters Man page
getClusters,ChromMaintainers-method Man page
getClusters-methods Man page
getRegionsInNetwork Man page
getRegionsInNetwork,ChromMaintainers,ChiapetExperimentData,numer Man page
getRegionsInNetwork-methods Man page
getRegionsIncluster Man page
getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numer Man page Man page
getRegionsIncluster-methods Man page
loadPETs Man page
loadPETs,ChiapetExperimentData,character-method Man page
loadPETs-methods Man page
loadPPI Man page
loadPPI,ChiapetExperimentData-method Man page
loadPPI-methods Man page
loadTFBS Man page
loadTFBS,ChiapetExperimentData Man page
loadTFBS,ChiapetExperimentData,character-method Man page
loadTFBS-methods Man page
networks Man page
networks,ChromMaintainers-method Man page
networks,NetworkCollection-method Man page
outputGenesPerClusterToDir Man page
outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentDat Man page Man page
outputGenesPerClusterToDir-methods Man page
outputGenesPerNetworkToDir Man page
outputGenesPerNetworkToDir,ChromMaintainers,ChiapetExperimentDat Man page
outputGenesPerNetworkToDir-methods Man page
pet Man page
pet,ChiapetExperimentData-method Man page
pet-methods Man page
pet<- Man page
pet<-,ChiapetExperimentData-method Man page
plot3CPETRes Man page
plot3CPETRes,ChromMaintainers-method Man page Man page
plot3CPETRes-methods Man page
plotTrack Man page
plotTrack,ChiapetExperimentData,GRanges-method Man page
plotTrack-methods Man page
ppi Man page
ppi,ChiapetExperimentData-method Man page
ppi-methods Man page
ppi<- Man page
ppi<-,ChiapetExperimentData-method Man page
sizes Man page
sizes,NetworkCollection-method Man page
tfbs Man page
tfbs,ChiapetExperimentData-method Man page
tfbs-methods Man page
tfbs<- Man page
tfbs<-,ChiapetExperimentData-method Man page
topEdges Man page
topEdges,ChromMaintainers-method Man page
topEdges-methods Man page
topNodes Man page
topNodes,ChromMaintainers-method Man page
topNodes-methods Man page
updateResults Man page
updateResults,ChromMaintainers,NetworkCollection,numeric-method Man page
updateResults-methods Man page
visualizeCircos Man page
visualizeCircos,ChromMaintainers,ChiapetExperimentData,numeric-m Man page Man page
visualizeCircos-methods Man page
visualizeInteractions Man page
visualizeInteractions,ChiapetExperimentData,GRanges-method Man page
visualizeInteractions-methods Man page
wordsPerTopic Man page
wordsPerTopic,HLDAResult-method Man page
wordsPerTopic-methods Man page
R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.

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