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-any)CBNplot_1.13.0.zip(r-4.6-any)CBNplot_1.13.0.zip(r-4.5-any)
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

4.83 score 68 stars 9 scripts 512 downloads 10 exports 156 dependencies

Last updated from:f259146285. Checks:1 NOTE, 7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	275
linux-devel	WARNING	439
source / vignettes	ERROR	388
linux-release	WARNING	514
macos-release	WARNING	455
macos-oldrel	WARNING	409
windows-devel	WARNING	349
windows-release	WARNING	418
windows-oldrel	WARNING	315
wasm-release	OK	187

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

Dependencies:abind 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 DelayedArray depmap digest dir.expiry distributional DOSE dplyr enrichit enrichplot evaluate ExperimentHub farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver fs gdtools generics GenomicRanges 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 MatrixGenerics matrixStats 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 S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo SparseArray stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidygraph tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridis viridisLite withr xfun XVector yaml yulab.utils

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

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