Package: R3CPET 1.39.0

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_1.39.0.tar.gz
R3CPET_1.39.0.zip(r-4.5)R3CPET_1.39.0.zip(r-4.4)R3CPET_1.39.0.zip(r-4.3)

R3CPET_1.39.0.tar.gz(r-4.5-noble)R3CPET_1.39.0.tar.gz(r-4.4-noble)
R3CPET.pdf |R3CPET.html✨
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:

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

On BioConductor:R3CPET-1.39.0(bioc 3.21)R3CPET-1.38.0(bioc 3.20)

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

5.62 score 4 stars 5 scripts 196 downloads 1 mentions 42 exports 157 dependencies

Last updated 2 months agofrom:adae88d8d1. Checks:OK: 1 WARNING: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	WARNING	Oct 31 2024
R-4.4-win-x86_64	WARNING	Oct 31 2024
R-4.3-win-x86_64	WARNING	Oct 31 2024

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 BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate class cli cluster clValid codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GGally ggbio ggplot2 ggstats glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl OrganismDbi patchwork pheatmap pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

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

Rendered fromR3CPET.Rnwusingknitr::knitron Oct 31 2024.

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