R3CPET
This is the development version of R3CPET; for the stable release version, see R3CPET.
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
Bioconductor version: Development (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("R3CPET")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, GenePrediction, GraphAndNetwork, HiC, Network, NetworkInference, Software |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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 |
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_1.39.0.tar.gz |
| Windows Binary (x86_64) | R3CPET_1.39.0.zip |
| 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 |