CBN2Path
This is the development version of CBN2Path; for the stable release version, see CBN2Path.
CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks
Bioconductor version: Development (3.24)
CBN2Path package provides a unifying interface to facilitate CBN-based quantification, analysis and visualization of cancer progression pathways.
Author: William Choi-Kim [aut, cre], Sayed-Rzgar Hosseini [aut, cre]
Maintainer: William Choi-Kim <william at williamck.com>, Sayed-Rzgar Hosseini <razgar at gmail.com>
citation("CBN2Path")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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("CBN2Path")
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("CBN2Path")| CBN2Path Vignette | HTML | R Script |
| Reference Manual | ||
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, GraphAndNetwork, Pathways, Software, StatisticalMethod |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr, igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks, BiocParallel |
| System Requirements | GNU Scientific Library (GSL) |
| URL | https://github.com/rockwillck/CBN2Path http://dx.doi.org/10.1093/biomet/asp023 http://dx.doi.org/10.1093/bioinformatics/btp505 |
| Bug Reports | https://github.com/rockwillck/CBN2Path/issues |
See More
| Suggests | testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown |
| Linking To | |
| 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 | CBN2Path_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | CBN2Path_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | CBN2Path_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CBN2Path |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CBN2Path |
| Bioc Package Browser | https://code.bioconductor.org/browse/CBN2Path/ |
| Package Short Url | https://bioconductor.org/packages/CBN2Path/ |
| Package Downloads Report | Download Stats |