Package: R3CPET 1.45.1

Mohamed Nadhir Djekidel

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

The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.

Authors:Djekidel MN, Yang Chen et al.

R3CPET_1.45.1.tar.gz
R3CPET_1.45.1.zip(r-4.7)R3CPET_1.45.1.zip(r-4.6)R3CPET_1.45.1.zip(r-4.5)

R3CPET_1.45.1.tar.gz(r-4.7-arm64)R3CPET_1.45.1.tar.gz(r-4.7-x86_64)R3CPET_1.45.1.tar.gz(r-4.6-arm64)R3CPET_1.45.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
R3CPET/json (API)
NEWS

# Install 'R3CPET' in R:
install.packages('R3CPET', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sirusb/r3cpet/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:R3CPET-1.45.0(bioc 3.24)R3CPET-1.44.0(bioc 3.23)

networkinferencegenepredictionbayesiangraphandnetworknetworkgeneexpressionhicchia-petchromatin-interactiondirichlet-process-mixturestranscription-factocpp

5.62 score 4 stars 8 scripts 372 downloads 1 mentions 42 exports 132 dependencies

Last updated from:43f1f69e0e. Checks:1 ERROR, 7 WARNING, 1 OK, 5 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR301
linux-devel-arm64WARNING466
linux-devel-x86_64WARNING556
source / vignettesOK435
linux-release-arm64WARNING463
linux-release-x86_64WARNING541
macos-release-arm64FAIL129
macos-release-x86_64FAIL265
macos-oldrel-arm64FAIL192
macos-oldrel-x86_64FAIL283
windows-develWARNING841
windows-releaseWARNING759
windows-oldrelWARNING787
wasm-releaseFAIL248

Exports:annotateExpressionbetasbuildNetworksChiapetExperimentDataChromMaintainersclusterInteractionsCreateCenteredBEDcreateIndexescreateServerdocPerTopicGenerateNetworksgetClustersgetRegionsInclustergetRegionsInNetworkGOEnrich.folderGOEnrich.networksHLDAResultInferNetworksloadPETsloadPPIloadTFBSNetworkCollectionnetworksoutputGenesPerClusterToDiroutputGenesPerNetworkToDirpetpet<-plot3CPETResplotTrackppippi<-PrepareDatasizesTFtfbstfbs<-topEdgestopNodesupdateResultsvisualizeCircosvisualizeInteractionswordsPerTopic

Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecigarilloclasscliclusterclValidcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydichromatdigestensembldbevaluatefarverfastmapfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggbioggplot2gluegraphgridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslOrganismDbipheatmappkgconfigplyrpngProtGenericsR6rappdirsRBGLRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystinytexUCSC.utilsVariantAnnotationvctrsviridisLitewithrxfunXMLXVectoryaml

3CPET: Finding Co-factor Complexes maintaining Chia-PET interactions

Rendered fromR3CPET.Rnwusingknitr::knitron May 29 2026.

Last update: 2020-10-03
Started: 2015-04-06

Readme and manuals

Help Manual

Help pageTopics
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet ProcessR3CPET-package R3CPET
Add the gene expression attribute to the graph nodesannotateExpression annotateExpression,ChromMaintainers,data.frame-method annotateExpression-methods
Biogrid NetworkBiogrid PPI.Biogrid
Building interaction networks connecting interacting regionsbuildNetworks buildNetworks,ChiapetExperimentData-method
3CPET used raw dataChiapetExperimentData ChiapetExperimentData-class pet pet,ChiapetExperimentData-method pet-methods pet<- pet<-,ChiapetExperimentData-method ppi ppi,ChiapetExperimentData-method ppi-methods ppi<- ppi<-,ChiapetExperimentData-method tfbs tfbs,ChiapetExperimentData-method tfbs-methods tfbs<- tfbs<-,ChiapetExperimentData-method
Chomatin maintainer networksChromMaintainers ChromMaintainers-class GenerateGmlNetworks GenerateGmlNetworks,ChromMaintainers-method GenerateGmlNetworks-methods getClusters getClusters,ChromMaintainers-method getClusters-methods networks,ChromMaintainers-method topEdges topEdges,ChromMaintainers-method topEdges-methods topNodes topNodes,ChromMaintainers-method topNodes-methods
Human chromosom lenghtsChromosoms chromosoms
Wrapper for 'clues' and 'sota' S3 classescluesOrSota-class
Grouping DNA interactions by enrichment profileclusterInteractions clusterInteractions,ChromMaintainers-method
Create centered interactionsCreateCenteredBED CreateCenteredBED,character-method CreateCenteredBED-methods
Preparing TF indexes per regioncreateIndexes createIndexes,ChiapetExperimentData-method createIndexes-methods
Explore results in a web browsercreateServer createServer,ChiapetExperimentData,NetworkCollection,ChromMaintainers-method createServer-methods
Ensemble to HGNC conversionEnsemblToHGNC
Entrez to HGNC conversionEntrezToHGNC
Nucleus located genesgeneLocations geneLocations.nucleus
Generate a list of 'igraph' networksGenerateNetworks GenerateNetworks,ChromMaintainers-method GenerateNetworks-methods
list of interactions per clustergetRegionsIncluster getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numeric-method getRegionsIncluster-methods
list of interactions per networkgetRegionsInNetwork getRegionsInNetwork,ChromMaintainers,ChiapetExperimentData,numeric-method getRegionsInNetwork-methods
GO enrichment methodsGOEnrich.folder GOEnrich.folder,character-method GOEnrich.folder-methods GOEnrich.networks GOEnrich.networks,ChromMaintainers-method GOEnrich.networks-methods
Class '"HLDAResult"'betas betas,HLDAResult-method betas-methods docPerTopic docPerTopic,HLDAResult-method docPerTopic-methods HLDAResult HLDAResult-class wordsPerTopic wordsPerTopic,HLDAResult-method wordsPerTopic-methods
HPRD protein interaction NetworkHPRD PPI.HPRD
Network construction using Hierarchical Dirichlet ProcessInferNetworks InferNetworks,NetworkCollection-method InferNetworks-methods
Parsing ChIA-PET interaction dataloadPETs loadPETs,ChiapetExperimentData,character-method loadPETs-methods
Setting the background protein-protein interactionloadPPI loadPPI,ChiapetExperimentData-method loadPPI-methods
Loading TF binding sitesloadTFBS loadTFBS,ChiapetExperimentData loadTFBS,ChiapetExperimentData,character-method loadTFBS-methods
protein interaction networks maintaining DNA loopsNetworkCollection NetworkCollection-class networks networks,NetworkCollection-method sizes sizes,NetworkCollection-method TF TF,NetworkCollection-method
List of genes in each clusteroutputGenesPerClusterToDir outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentData-method outputGenesPerClusterToDir-methods
List of genes controlled by each networkoutputGenesPerNetworkToDir outputGenesPerNetworkToDir,ChromMaintainers,ChiapetExperimentData-method outputGenesPerNetworkToDir-methods
Plotting clustering resultsplot3CPETRes plot3CPETRes,ChromMaintainers-method plot3CPETRes-methods
Plot interaction on a genomic trackplotTrack plotTrack,ChiapetExperimentData,GRanges-method plotTrack-methods
Loading the raw data all at oncePrepareData PrepareData,character,character,logical-method PrepareData-methods
A gene expression datasetRPKMS
update top maintain networks elementsupdateResults updateResults,ChromMaintainers,NetworkCollection,numeric-method updateResults-methods
Generate circos plot per clustervisualizeCircos visualizeCircos,ChromMaintainers,ChiapetExperimentData,numeric-method visualizeCircos-methods
Display a Circos plot of ChIA-pet interactionsvisualizeInteractions visualizeInteractions,ChiapetExperimentData,GRanges-method visualizeInteractions-methods