Package: punKEGGer 0.99.65

Guillermo de Anda Jáuregui

punKEGGer: Parse, Expand, Annotate and Visualize KEGG Pathway Networks as Tidy Graphs

Provides tools to parse KEGG pathway KGML files into tidy graphs, expand metanodes (e.g., multi-gene entries), annotate them with custom dictionaries, and produce consistent visualizations using ggraph. Enables integration of KEGG pathways with tidygraph-based workflows.

Authors:Guillermo de Anda Jáuregui [aut, cre]

punKEGGer_0.99.65.tar.gz
punKEGGer_0.99.65.zip(r-4.7-any)punKEGGer_0.99.65.zip(r-4.6-any)punKEGGer_0.99.65.zip(r-4.5-any)
punKEGGer_0.99.65.tgz(r-4.6-any)punKEGGer_0.99.65.tgz(r-4.5-any)
punKEGGer_0.99.65.tar.gz(r-4.7-any)punKEGGer_0.99.65.tar.gz(r-4.6-any)
punKEGGer_0.99.65.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
punKEGGer/json (API)

# Install 'punKEGGer' in R:

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

Bug tracker:https://github.com/guillermodeandajauregui/punkegger/issues

On CRAN:

pathways graphandnetwork software network visualization kegg

3.00 score 1 stars 11 exports 66 dependencies

Last updated from:68a8e2d60f. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	196
linux-devel	OK	311
source / vignettes	OK	215
linux-release	OK	272
macos-release	OK	168
macos-oldrel	OK	212
windows-devel	OK	89
windows-release	OK	101
windows-oldrel	OK	101
wasm-release	OK	128

Exports:add_kegg_layout annotate_kegg_graph combine_kegg_network create_meta_dict expand_metagraph extract_kegg_nodes fetch_kegg_kgml layout_kegg parse_kegg_groups parse_kegg_relations_clean plot_kegg_graph

Dependencies:askpass base64enc BiocGenerics Biostrings cachem cli cpp11 crayon curl dplyr farver fastmap generics ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable httr igraph IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix memoise mime openssl pillar pkgconfig png polyclip purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S4Vectors S7 scales Seqinfo stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr xml2 XVector

punKEGGer: parsing and visualization of KEGG pathways for network science

Rendered frompunkegger-vignette-bioconductor.Rmdusingknitr::rmarkdown

Last update: 2026-07-10
Started: 2025-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add KEGG layout coordinates to a tidygraph	add_kegg_layout
Annotate a KEGG tidygraph with custom identifiers	annotate_kegg_graph
Combine KEGG group and relation edges into a tidygraph	combine_kegg_network
Create a meta_id-to-annotation dictionary	create_meta_dict
Expand a KEGG tidygraph by unrolling multi-gene metanodes	expand_metagraph
Extract KEGG node information from a KGML file	extract_kegg_nodes
Fetch a KEGG pathway KGML via KEGGREST	fetch_kegg_kgml
Extract node layout coordinates from a KEGG KGML file	layout_kegg
Parse KEGG group nodes from a KGML file	parse_kegg_groups
Parse clean KEGG relations from a KGML file	parse_kegg_relations_clean
Visualize a KEGG pathway tidygraph using manual layout	plot_kegg_graph