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.

AuthorDjekidel MN, Yang Chen et al.
Date of publicationNone
MaintainerMohamed Nadhir Djekidel <djek.nad@gmail.com>
LicenseGPL (>=2)
Version1.6.0
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

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

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