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