R3CPET

This package is for version 3.21 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: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, GeneExpression, GenePrediction, GraphAndNetwork, HiC, Network, NetworkInference, Software

Version 1.40.0

In Bioconductor since BioC 3.1 (R-3.2) (10.5 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

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

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Package Archives

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

Source Package R3CPET_1.40.0.tar.gz

Windows Binary (x86_64) R3CPET_1.40.0.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/

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