Package: CBNplot 1.13.0

Noriaki Sato

CBNplot: plot bayesian network inferred from gene expression data based on enrichment analysis results

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.

Authors:Noriaki Sato [cre, aut]

CBNplot_1.13.0.tar.gz
CBNplot_1.13.0.zip(r-4.7)CBNplot_1.13.0.zip(r-4.6)CBNplot_1.13.0.zip(r-4.5)
CBNplot_1.13.0.tgz(r-4.6-any)CBNplot_1.13.0.tgz(r-4.5-any)
CBNplot_1.13.0.tar.gz(r-4.7-any)CBNplot_1.13.0.tar.gz(r-4.6-any)
CBNplot_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CBNplot/json (API)

# Install 'CBNplot' in R:

install.packages('CBNplot', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/noriakis/cbnplot/issues

Datasets:

exampleEaRes - Example enrichment analysis result
exampleGeneExp - Example gene expression data

On BioConductor:CBNplot-1.13.0(bioc 3.24)CBNplot-1.12.0(bioc 3.23)

visualization bayesian geneexpression networkinference pathways reactome network networkenrichment genesetenrichment

6.13 score 68 stars 8 scripts 10 exports 148 dependencies

Last updated from:f259146285. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	314
linux-devel-x86_64	OK	557
source / vignettes	OK	387
linux-release-x86_64	OK	556
macos-release-arm64	OK	251
macos-oldrel-arm64	OK	264
windows-devel	OK	420
windows-release	OK	466
windows-oldrel	OK	505
wasm-release	OK	291

Exports:bngeneplot bngeneplotCustom bngenetest bnpathplot bnpathplotCustom bnpathtest compareBNs obtainPath queryCpDistLs queryCpDistLw

Dependencies:aisdk AnnotationDbi AnnotationHub ape aplot askpass base64enc Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bnlearn bslib cachem callr cli cluster clusterProfiler cpp11 crayon curl DBI dbplyr depmap digest dir.expiry distributional DOSE dplyr enrichit enrichplot evaluate ExperimentHub farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics ggdist ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree glue gmp GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lazyeval lifecycle magrittr MASS Matrix memoise mime nlme numDeriv openssl org.Hs.eg.db otel patchwork pillar pkgconfig plyr png polyclip processx ps purrr pvclust quadprog qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang rmarkdown Rmpfr RSQLite S4Vectors S7 sass scales scatterpie Seqinfo stringi stringr sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridis viridisLite withr xfun XVector yaml yulab.utils

CBNplot

Rendered fromCBNplot_basic_usage.Rmdusingknitr::rmarkdown

Last update: 2024-10-02
Started: 2022-02-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
bngeneplot	bngeneplot
bngeneplotCustom	bngeneplotCustom
bngenetest	bngenetest
bnpathplot	bnpathplot
bnpathplotCustom	bnpathplotCustom
bnpathtest	bnpathtest
compareBNs	compareBNs
Example enrichment analysis result	exampleEaRes
Example gene expression data	exampleGeneExp
inferMS	inferMS
loadSign	loadSign
obtainPath	obtainPath
queryCpDistLs	queryCpDistLs
queryCpDistLw	queryCpDistLw