R3CPET

This is the development version of R3CPET; for the stable release version, see R3CPET.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

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

Bioconductor version: Development (3.24)

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")):

Djekidel MN, Yang Chen et al. R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process. doi:10.18129/B9.bioc.R3CPET, R package version 1.45.1, https://bioconductor.org/packages/R3CPET.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bayesian, GeneExpression, GenePrediction, GraphAndNetwork, HiC, Network, NetworkInference, Software
Version	1.45.1
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 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
System Requirements
URL	https://github.com/sirusb/R3CPET
Bug Reports	https://github.com/sirusb/R3CPET/issues

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, r-universe

Package Archives

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

Source Package	R3CPET_1.45.1.tar.gz
Windows Binary (x86_64)	R3CPET_1.45.1.zip
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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	https://bioconductor.org/packages/R3CPET/
Package Downloads Report	Download Stats