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R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Bioconductor version: Release (3.17)

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.

Maintainer: Mohamed Nadhir Djekidel <djek.nad at gmail.com>

Citation (from within R, enter citation("R3CPET")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("R3CPET")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("R3CPET")
3CPET: Finding Co-factor Complexes maintaining Chia-PET interactions PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, GeneExpression, GenePrediction, GraphAndNetwork, HiC, Network, NetworkInference, Software
Version 1.32.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL (>=2)
Depends R (>= 3.2), Rcpp (>= 0.10.4), methods
Imports methods, parallel, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges(>= 2.13.12), GenomeInfoDb, GenomicRanges(>= 1.31.8), ggbio
Linking To Rcpp
Suggests BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno
System Requirements
Enhances
URL
Bug Reports https://github.com/sirusb/R3CPET/issues
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package R3CPET_1.32.0.tar.gz
Windows Binary R3CPET_1.32.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64) R3CPET_1.31.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/R3CPET
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/R3CPET
Bioc Package Browser https://code.bioconductor.org/browse/R3CPET/
Package Short Url https://bioconductor.org/packages/R3CPET/
Package Downloads Report Download Stats