A B C D E G H I L N O P R S T U V W
R3CPET-package | 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process |
annotateExpression | Add the gene expression attribute to the graph nodes |
annotateExpression-method | Add the gene expression attribute to the graph nodes |
annotateExpression-methods | Add the gene expression attribute to the graph nodes |
betas | Class '"HLDAResult"' |
betas-method | Class '"HLDAResult"' |
betas-methods | Class '"HLDAResult"' |
Biogrid | Biogrid Network |
buildNetworks | Building interaction networks connecting interacting regions |
buildNetworks-method | Building interaction networks connecting interacting regions |
ChiapetExperimentData | 3CPET used raw data |
ChiapetExperimentData-class | 3CPET used raw data |
ChromMaintainers | Chomatin maintainer networks |
ChromMaintainers-class | Chomatin maintainer networks |
Chromosoms | Human chromosom lenghts |
chromosoms | Human chromosom lenghts |
cluesOrSota-class | Wrapper for 'clues' and 'sota' S3 classes |
clusterInteractions | Grouping DNA interactions by enrichment profile |
clusterInteractions-method | Grouping DNA interactions by enrichment profile |
CreateCenteredBED | Create centered interactions |
CreateCenteredBED-method | Create centered interactions |
CreateCenteredBED-methods | Create centered interactions |
createIndexes | Preparing TF indexes per region |
createIndexes-method | Preparing TF indexes per region |
createIndexes-methods | Preparing TF indexes per region |
createServer | Explore results in a web browser |
createServer-method | Explore results in a web browser |
createServer-methods | Explore results in a web browser |
docPerTopic | Class '"HLDAResult"' |
docPerTopic-method | Class '"HLDAResult"' |
docPerTopic-methods | Class '"HLDAResult"' |
EnsemblToHGNC | Ensemble to HGNC conversion |
EntrezToHGNC | Entrez to HGNC conversion |
geneLocations | Nucleus located genes |
geneLocations.nucleus | Nucleus located genes |
GenerateGmlNetworks | Chomatin maintainer networks |
GenerateGmlNetworks-method | Chomatin maintainer networks |
GenerateGmlNetworks-methods | Chomatin maintainer networks |
GenerateNetworks | Generate a list of 'igraph' networks |
GenerateNetworks-method | Generate a list of 'igraph' networks |
GenerateNetworks-methods | Generate a list of 'igraph' networks |
getClusters | Chomatin maintainer networks |
getClusters-method | Chomatin maintainer networks |
getClusters-methods | Chomatin maintainer networks |
getRegionsIncluster | list of interactions per cluster |
getRegionsIncluster-method | list of interactions per cluster |
getRegionsIncluster-methods | list of interactions per cluster |
getRegionsInNetwork | list of interactions per network |
getRegionsInNetwork-method | list of interactions per network |
getRegionsInNetwork-methods | list of interactions per network |
GOEnrich.folder | GO enrichment methods |
GOEnrich.folder-method | GO enrichment methods |
GOEnrich.folder-methods | GO enrichment methods |
GOEnrich.networks | GO enrichment methods |
GOEnrich.networks-method | GO enrichment methods |
GOEnrich.networks-methods | GO enrichment methods |
HLDAResult | Class '"HLDAResult"' |
HLDAResult-class | Class '"HLDAResult"' |
HPRD | HPRD protein interaction Network |
InferNetworks | Network construction using Hierarchical Dirichlet Process |
InferNetworks-method | Network construction using Hierarchical Dirichlet Process |
InferNetworks-methods | Network construction using Hierarchical Dirichlet Process |
loadPETs | Parsing ChIA-PET interaction data |
loadPETs-method | Parsing ChIA-PET interaction data |
loadPETs-methods | Parsing ChIA-PET interaction data |
loadPPI | Setting the background protein-protein interaction |
loadPPI-method | Setting the background protein-protein interaction |
loadPPI-methods | Setting the background protein-protein interaction |
loadTFBS | Loading TF binding sites |
loadTFBS,ChiapetExperimentData | Loading TF binding sites |
loadTFBS-method | Loading TF binding sites |
loadTFBS-methods | Loading TF binding sites |
NetworkCollection | protein interaction networks maintaining DNA loops |
NetworkCollection-class | protein interaction networks maintaining DNA loops |
networks | protein interaction networks maintaining DNA loops |
networks-method | Chomatin maintainer networks |
networks-method | protein interaction networks maintaining DNA loops |
outputGenesPerClusterToDir | List of genes in each cluster |
outputGenesPerClusterToDir-method | List of genes in each cluster |
outputGenesPerClusterToDir-methods | List of genes in each cluster |
outputGenesPerNetworkToDir | List of genes controlled by each network |
outputGenesPerNetworkToDir-method | List of genes controlled by each network |
outputGenesPerNetworkToDir-methods | List of genes controlled by each network |
pet | 3CPET used raw data |
pet-method | 3CPET used raw data |
pet-methods | 3CPET used raw data |
pet<- | 3CPET used raw data |
pet<--method | 3CPET used raw data |
plot3CPETRes | Plotting clustering results |
plot3CPETRes-method | Plotting clustering results |
plot3CPETRes-methods | Plotting clustering results |
plotTrack | Plot interaction on a genomic track |
plotTrack-method | Plot interaction on a genomic track |
plotTrack-methods | Plot interaction on a genomic track |
ppi | 3CPET used raw data |
ppi-method | 3CPET used raw data |
ppi-methods | 3CPET used raw data |
PPI.Biogrid | Biogrid Network |
PPI.HPRD | HPRD protein interaction Network |
ppi<- | 3CPET used raw data |
ppi<--method | 3CPET used raw data |
PrepareData | Loading the raw data all at once |
PrepareData-method | Loading the raw data all at once |
PrepareData-methods | Loading the raw data all at once |
R3CPET | 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process |
RPKMS | A gene expression dataset |
sizes | protein interaction networks maintaining DNA loops |
sizes-method | protein interaction networks maintaining DNA loops |
TF | protein interaction networks maintaining DNA loops |
TF-method | protein interaction networks maintaining DNA loops |
tfbs | 3CPET used raw data |
tfbs-method | 3CPET used raw data |
tfbs-methods | 3CPET used raw data |
tfbs<- | 3CPET used raw data |
tfbs<--method | 3CPET used raw data |
topEdges | Chomatin maintainer networks |
topEdges-method | Chomatin maintainer networks |
topEdges-methods | Chomatin maintainer networks |
topNodes | Chomatin maintainer networks |
topNodes-method | Chomatin maintainer networks |
topNodes-methods | Chomatin maintainer networks |
updateResults | update top maintain networks elements |
updateResults-method | update top maintain networks elements |
updateResults-methods | update top maintain networks elements |
visualizeCircos | Generate circos plot per cluster |
visualizeCircos-method | Generate circos plot per cluster |
visualizeCircos-methods | Generate circos plot per cluster |
visualizeInteractions | Display a Circos plot of ChIA-pet interactions |
visualizeInteractions-method | Display a Circos plot of ChIA-pet interactions |
visualizeInteractions-methods | Display a Circos plot of ChIA-pet interactions |
wordsPerTopic | Class '"HLDAResult"' |
wordsPerTopic-method | Class '"HLDAResult"' |
wordsPerTopic-methods | Class '"HLDAResult"' |