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R3CPET

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


Bioconductor version: Release (3.18)

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 1.34.1
In Bioconductor since BioC 3.1 (R-3.2) (9 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
System Requirements
URL
Bug Reports https://github.com/sirusb/R3CPET/issues
See More
Suggests BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package R3CPET_1.34.1.tar.gz
Windows Binary R3CPET_1.34.1.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
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
Old Source Packages for BioC 3.18 Source Archive