Package: CBNplot 1.7.0

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_1.7.0.tar.gz
CBNplot_1.7.0.zip(r-4.5)CBNplot_1.7.0.zip(r-4.4)
CBNplot_1.7.0.tgz(r-4.4-any)
CBNplot_1.7.0.tar.gz(r-4.5-noble)CBNplot_1.7.0.tar.gz(r-4.4-noble)
CBNplot_1.7.0.tgz(r-4.4-emscripten)
CBNplot.pdf |CBNplot.html✨
CBNplot/json (API)
NEWS

# 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-1.7.0(bioc 3.21)CBNplot-1.6.0(bioc 3.20)

visualization bayesian geneexpression networkinference pathways reactome network networkenrichment genesetenrichment

6.49 score 62 stars 9 scripts 258 downloads 10 exports 142 dependencies

Last updated 2 months agofrom:5dcddfc6ff. Checks:OK: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	OK	Dec 19 2024
R-4.5-linux	OK	Dec 19 2024
R-4.4-win	OK	Dec 19 2024
R-4.4-mac	OK	Dec 19 2024

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

Dependencies:AnnotationDbi AnnotationHub ape aplot askpass BH Biobase BiocFileCache BiocGenerics BiocManager BiocParallel BiocVersion Biostrings bit bit64 blob bnlearn cachem cli clusterProfiler codetools colorspace cowplot cpp11 crayon curl data.table DBI dbplyr depmap digest distributional DOSE dplyr enrichplot ExperimentHub fansi farver fastmap fastmatch fgsea filelock formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData ggdist ggforce ggfun ggnewscale ggplot2 ggplotify ggraph ggrepel ggtangle ggtree glue gmp GO.db GOSemSim graph graphite graphlayouts gridExtra gridGraphics gson gtable httr httr2 igraph IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme numDeriv openssl org.Hs.eg.db patchwork pillar pkgconfig plogr plyr png polyclip purrr pvclust quadprog qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reshape2 rlang Rmpfr RSQLite S4Vectors scales scatterpie snow stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vctrs viridis viridisLite withr XVector yaml yulab.utils zlibbioc

CBNplot

Rendered fromCBNplot_basic_usage.Rmdusingknitr::rmarkdownon Dec 19 2024.

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