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✨
DESCRIPTION |NEWS
card.svg |card.png
R3CPET/json (API)

# 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:

Chromosoms - Human chromosom lenghts
geneLocations.nucleus - Nucleus located genes
PPI.Biogrid - Biogrid Network
PPI.HPRD - HPRD protein interaction Network
RPKMS - A gene expression dataset

On BioConductor:R3CPET-1.45.1(bioc 3.24)R3CPET-1.44.0(bioc 3.23)

networkinference geneprediction bayesian graphandnetwork network geneexpression hic chia-pet chromatin-interaction dirichlet-process-mixtures transcription-facto cpp

5.62 score 4 stars 6 scripts 1 mentions 42 exports 132 dependencies

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

Target	Result	Time
bioc-checks	ERROR	306
linux-devel-arm64	WARNING	438
linux-devel-x86_64	WARNING	517
source / vignettes	OK	466
linux-release-arm64	WARNING	427
linux-release-x86_64	WARNING	508
macos-release-arm64	FAIL	118
macos-release-x86_64	FAIL	282
macos-oldrel-arm64	FAIL	89
macos-oldrel-x86_64	FAIL	217
windows-devel	WARNING	534
windows-release	WARNING	498
windows-oldrel	WARNING	462
wasm-release	FAIL	270

Exports:annotateExpression betas buildNetworks ChiapetExperimentData ChromMaintainers clusterInteractions CreateCenteredBED createIndexes createServer docPerTopic GenerateNetworks getClusters getRegionsIncluster getRegionsInNetwork GOEnrich.folder GOEnrich.networks HLDAResult InferNetworks loadPETs loadPPI loadTFBS NetworkCollection networks outputGenesPerClusterToDir outputGenesPerNetworkToDir pet pet<-plot3CPETRes plotTrack ppi ppi<-PrepareData sizes TF tfbs tfbs<-topEdges topNodes updateResults visualizeCircos visualizeInteractions wordsPerTopic

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo class cli cluster clValid codetools colorspace cpp11 crayon curl data.table DBI DelayedArray dichromat digest ensembldb evaluate farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 glue graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnet openssl OrganismDbi pheatmap pkgconfig plyr png ProtGenerics R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tinytex UCSC.utils VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml

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

1 Introduction | 2 Using R3CPET | 3 Session Info

Rendered fromR3CPET.Rnwusingknitr::knitr

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process	R3CPET-package R3CPET
Add the gene expression attribute to the graph nodes	annotateExpression annotateExpression,ChromMaintainers,data.frame-method annotateExpression-methods
Biogrid Network	Biogrid PPI.Biogrid
Building interaction networks connecting interacting regions	buildNetworks buildNetworks,ChiapetExperimentData-method
3CPET used raw data	ChiapetExperimentData 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 networks	ChromMaintainers 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 lenghts	Chromosoms chromosoms
Wrapper for 'clues' and 'sota' S3 classes	cluesOrSota-class
Grouping DNA interactions by enrichment profile	clusterInteractions clusterInteractions,ChromMaintainers-method
Create centered interactions	CreateCenteredBED CreateCenteredBED,character-method CreateCenteredBED-methods
Preparing TF indexes per region	createIndexes createIndexes,ChiapetExperimentData-method createIndexes-methods
Explore results in a web browser	createServer createServer,ChiapetExperimentData,NetworkCollection,ChromMaintainers-method createServer-methods
Ensemble to HGNC conversion	EnsemblToHGNC
Entrez to HGNC conversion	EntrezToHGNC
Nucleus located genes	geneLocations geneLocations.nucleus
Generate a list of 'igraph' networks	GenerateNetworks GenerateNetworks,ChromMaintainers-method GenerateNetworks-methods
list of interactions per cluster	getRegionsIncluster getRegionsIncluster,ChromMaintainers,ChiapetExperimentData,numeric-method getRegionsIncluster-methods
list of interactions per network	getRegionsInNetwork getRegionsInNetwork,ChromMaintainers,ChiapetExperimentData,numeric-method getRegionsInNetwork-methods
GO enrichment methods	GOEnrich.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 Network	HPRD PPI.HPRD
Network construction using Hierarchical Dirichlet Process	InferNetworks InferNetworks,NetworkCollection-method InferNetworks-methods
Parsing ChIA-PET interaction data	loadPETs loadPETs,ChiapetExperimentData,character-method loadPETs-methods
Setting the background protein-protein interaction	loadPPI loadPPI,ChiapetExperimentData-method loadPPI-methods
Loading TF binding sites	loadTFBS loadTFBS,ChiapetExperimentData loadTFBS,ChiapetExperimentData,character-method loadTFBS-methods
protein interaction networks maintaining DNA loops	NetworkCollection NetworkCollection-class networks networks,NetworkCollection-method sizes sizes,NetworkCollection-method TF TF,NetworkCollection-method
List of genes in each cluster	outputGenesPerClusterToDir outputGenesPerClusterToDir,ChromMaintainers,ChiapetExperimentData-method outputGenesPerClusterToDir-methods
List of genes controlled by each network	outputGenesPerNetworkToDir outputGenesPerNetworkToDir,ChromMaintainers,ChiapetExperimentData-method outputGenesPerNetworkToDir-methods
Plotting clustering results	plot3CPETRes plot3CPETRes,ChromMaintainers-method plot3CPETRes-methods
Plot interaction on a genomic track	plotTrack plotTrack,ChiapetExperimentData,GRanges-method plotTrack-methods
Loading the raw data all at once	PrepareData PrepareData,character,character,logical-method PrepareData-methods
A gene expression dataset	RPKMS
update top maintain networks elements	updateResults updateResults,ChromMaintainers,NetworkCollection,numeric-method updateResults-methods
Generate circos plot per cluster	visualizeCircos visualizeCircos,ChromMaintainers,ChiapetExperimentData,numeric-method visualizeCircos-methods
Display a Circos plot of ChIA-pet interactions	visualizeInteractions visualizeInteractions,ChiapetExperimentData,GRanges-method visualizeInteractions-methods