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.

Author
Djekidel MN, Yang Chen et al.
Date of publication
None
Maintainer
Mohamed Nadhir Djekidel <djek.nad@gmail.com>
License
GPL (>=2)
Version
1.6.0
URLs

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

Files in this package

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