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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("R3CPET")
AuthorDjekidel MN, Yang Chen et al.
Bioconductor views Bayesian GeneExpression GenePrediction GraphAndNetwork HiC Network NetworkInference
Date of publicationNone
MaintainerMohamed Nadhir Djekidel <djek.nad@gmail.com>
LicenseGPL (>=2)
Version1.8.0
https://github.com/sirusb/R3CPET

View on Bioconductor

Man pages

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

Functions

annotateExpression Man page
annotateExpression,ChromMaintainers,data.frame-method Man page
annotateExpression,ChromMaintainers,data.frame-method Man page
annotateExpression-methods Man page
betas Man page
betas,HLDAResult-method Man page
betas-methods Man page
Biogrid Man page
buildNetworks Man page
buildNetworks,ChiapetExperimentData-method Man page
ChiapetExperimentData Man page
ChiapetExperimentData-class Man page
ChromMaintainers Man page
ChromMaintainers-class Man page
chromosoms Man page
Chromosoms Man page
cluesOrSota-class Man page
cluster,ChromMaintainers-method Man page
clusterInteractions Man page
clusterInteractions,ChromMaintainers-method Man page
CreateCenteredBED Man page
CreateCenteredBED,character-method Man page
CreateCenteredBED-methods 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
EnsemblToHGNC Man page
EntrezToHGNC Man page
geneLocations Man page
geneLocations.nucleus 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
getClusters Man page
getClusters,ChromMaintainers-method Man page
getClusters-methods Man page
getRegionsIncluster Man page
getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numer Man page
getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numer Man page
getRegionsIncluster-methods Man page
getRegionsInNetwork Man page
getRegionsInNetwork,ChromMaintainers,ChiapetExperimentData,numer Man page
getRegionsInNetwork-methods Man page
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
HLDAResult Man page
HLDAResult-class Man page
HPRD Man page
InferNetworks Man page
InferNetworks-methods Man page
InferNetworks,NetworkCollection-method 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
NetworkCollection Man page
NetworkCollection-class Man page
networks Man page
networks,ChromMaintainers-method Man page
networks,NetworkCollection-method Man page
outputGenesPerClusterToDir Man page
outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentDat Man page
outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentDat Man page
outputGenesPerClusterToDir-methods Man page
outputGenesPerNetworkToDir Man page
outputGenesPerNetworkToDir,ChromMaintainers,ChiapetExperimentDat Man page
outputGenesPerNetworkToDir-methods Man page
pet Man page
pet<- Man page
pet<-,ChiapetExperimentData-method Man page
pet,ChiapetExperimentData-method Man page
pet-methods Man page
plot3CPETRes Man page
plot3CPETRes,ChromMaintainers-method Man page
plot3CPETRes,ChromMaintainers-method Man page
plot3CPETRes-methods Man page
plotTrack Man page
plotTrack,ChiapetExperimentData,GRanges-method Man page
plotTrack-methods Man page
ppi Man page
ppi<- Man page
PPI.Biogrid Man page
ppi<-,ChiapetExperimentData-method Man page
ppi,ChiapetExperimentData-method Man page
PPI.HPRD Man page
ppi-methods 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
sizes Man page
sizes,NetworkCollection-method Man page
TF Man page
tfbs Man page
tfbs<- Man page
tfbs<-,ChiapetExperimentData-method Man page
tfbs,ChiapetExperimentData-method Man page
tfbs-methods Man page
TF,NetworkCollection-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
visualizeCircos,ChromMaintainers,ChiapetExperimentData,numeric-m 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

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.r R/AllGenerics.r R/ChiapetExperimentData-methods.r R/ChromMaintainers-methods.r R/DAVIDQuery.r R/HLDAResult-methods.R R/NetworkCollection-methods.r R/PrepareData.r R/RcppExports.R R/WebGenerator-methods.r R/helper-DavidGOEnrich.R R/helper-GeneNameConversion.R R/helpers-utils.R
README.md
build
build/vignette.rds
data
data/Biogrid.RData
data/HPRD.RData
data/RPKMS.RData
data/chromosoms.RData
data/datalist
data/geneLocations.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/R3CPET.R
inst/doc/R3CPET.Rnw
inst/doc/R3CPET.pdf
inst/example
inst/example/HepG2_TF.txt.gz
inst/example/HepG2_centered.bed
inst/example/HepG2_interactions.txt
inst/example/hlda.RData
inst/example/nets.RData
inst/www
inst/www/d3.min.js
inst/www/graph.js
inst/www/server.R inst/www/ui.R
man
man/Biogrid.Rd man/ChiapetExperimentData-class.Rd man/ChromMaintainers-class.Rd man/CreateCenteredBED-methods.Rd man/EnsemblToHGNC.Rd man/EntrezToHGNC.Rd man/GOEnrich-methods.Rd man/GenerateNetworks-methods.Rd man/HLDAResult-class.Rd man/HPRD.Rd man/InferNetworks-methods.Rd man/NetworkCollection-class.Rd man/PrepareData-methods.Rd man/R3CPET-package.Rd man/RPKMS.Rd man/annotateExpression-methods.Rd man/buildNetworks-methods.Rd man/chromosoms.Rd man/cluesOrSota-class.Rd man/clusterInteractions-methods.Rd man/createIndexes-methods.Rd man/createServer-methods.Rd man/geneLocations.Rd man/getRegionsInNetwork-methods.Rd man/getRegionsIncluster-methods.Rd man/loadPETs-methods.Rd man/loadPPI-methods.Rd man/loadTFBS-methods.Rd man/outputGenesPerClusterToDir-methods.Rd man/outputGenesPerNetworkToDir-methods.Rd man/plotRes-methods.Rd man/plotTrack.Rd man/updateResults-methods.Rd man/visualizeCircos-methods.Rd man/visualizeInteractions-methods.Rd
src
src/Makevars
src/Makevars.win
src/R3CPET_init.c
src/RcppExports.cpp
src/corpus.cpp
src/corpus.h
src/main.cpp
src/state.cpp
src/state.h
src/stirln.cpp
src/stirln.h
src/utils.cpp
src/utils.h
tests
tests/tests.R
vignettes
vignettes/HLDA.pdf
vignettes/Network_Construction.png
vignettes/NetworksEnrich.pdf
vignettes/R3CPET.Rnw
vignettes/cluster_GO.png
vignettes/rawData_selection.png
vignettes/resultsClusters_selection.png
vignettes/resultsNetwork_selection.png
vignettes/resultsNetworks_3ds.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.