CBNplot
This is the released version of CBNplot; for the devel version, see CBNplot.
plot bayesian network inferred from gene expression data based on enrichment analysis results
Bioconductor version: Release (3.23)
This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.
Author: Noriaki Sato [cre, aut]
Maintainer: Noriaki Sato <nori at hgc.jp>
citation("CBNplot")):
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")
BiocManager::install("CBNplot")
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("CBNplot")| CBNplot | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, GeneExpression, GeneSetEnrichment, Network, NetworkEnrichment, NetworkInference, Pathways, Reactome, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0) |
| Imports | ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7), patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot, reshape2, ggforce, dplyr, tidyr, stringr, depmap, ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist, purrr, pvclust, stats, rlang |
| System Requirements | |
| URL | https://github.com/noriakis/CBNplot |
| Bug Reports | https://github.com/noriakis/CBNplot/issues |
See More
| Suggests | knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) |
| 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 | CBNplot_1.12.0.tar.gz |
| Windows Binary (x86_64) | CBNplot_1.12.0.zip |
| macOS Binary (big-sur-x86_64) | CBNplot_1.12.0.tgz |
| macOS Binary (sonoma-arm64) | CBNplot_1.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CBNplot |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CBNplot |
| Bioc Package Browser | https://code.bioconductor.org/browse/CBNplot/ |
| Package Short Url | https://bioconductor.org/packages/CBNplot/ |
| Package Downloads Report | Download Stats |