R3CPET

DOI: 10.18129/B9.bioc.R3CPET    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see R3CPET.

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

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	3CPET: Finding Co-factor Complexes maintaining Chia-PET interactions
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, GeneExpression, GenePrediction, GraphAndNetwork, HiC, Network, NetworkInference, Software
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 years)
License	GPL (>=2)
Depends	R (>= 3.2), Rcpp (>= 0.10.4), methods
Imports	methods, parallel, clues, ggplot2, pheatmap, clValid, igraph, data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors, IRanges(>= 2.13.12), GenomeInfoDb, GenomicRanges(>= 1.31.8), ggbio
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno
SystemRequirements
Enhances
URL
BugReports	https://github.com/sirusb/R3CPET/issues
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_1.14.0.tar.gz
Windows Binary	R3CPET_1.14.0.zip
Mac OS X 10.11 (El Capitan)	R3CPET_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/R3CPET
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/R3CPET
Package Short Url	http://bioconductor.org/packages/R3CPET/
Package Downloads Report	Download Stats