Package: KEGGemUP 0.99.1

Federico Marini

KEGGemUP: Creating, Rendering, and Mapping Omics Data on KEGG Pathway Graphs

KEGGemUP retrieves and renders interactively KEGG pathway graphs. The retrieval makes full use of the caching functionality to avoid unnecessary download processes. The interactivity of the graph is warranted via the visNetwork interface to the vis.js library, fully supporting bindings to be used in Shiny for further operations.

Authors:Edoardo Filippi [aut], Myriam Meineck [ctb], Paul Classen [ctb], Julia Weinmann-Menke [fnd], Federico Marini [aut, cre]

KEGGemUP_0.99.1.tar.gz
KEGGemUP_0.99.1.zip(r-4.7)KEGGemUP_0.99.1.zip(r-4.6)KEGGemUP_0.99.1.zip(r-4.5)
KEGGemUP_0.99.1.tgz(r-4.6-any)KEGGemUP_0.99.1.tgz(r-4.5-any)
KEGGemUP_0.99.1.tar.gz(r-4.7-any)KEGGemUP_0.99.1.tar.gz(r-4.6-any)
KEGGemUP_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
KEGGemUP/json (API)
NEWS

# Install 'KEGGemUP' in R:

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

Bug tracker:https://github.com/imbeimainz/keggemup/issues

Datasets:

res_de_macro_IFNg_vs_naive - A sample 'data.frame' containing Differential Expression Analysis, generated with 'limma'

On BioConductor:KEGGemUP-0.99.1(bioc 3.24)

software pathways kegg network visualization differentialexpression graphandnetwork transcriptomics proteomics metabolomics systemsbiology

5.13 score 2 scripts 12 exports 79 dependencies

Last updated from:b905e7ac43. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	190
linux-devel-x86_64	ERROR	341
source / vignettes	OK	249
linux-release-x86_64	ERROR	303
macos-release-arm64	ERROR	216
macos-oldrel-arm64	ERROR	189
windows-devel	ERROR	222
windows-release	ERROR	232
windows-oldrel	ERROR	218
wasm-release	OK	127

Exports:cleanup_title_node create_kegg_graph display_cache_KEGGemUP export_kegg_graph get_kegg_db highlight_kegg_graph map_results_to_graph render_kegg_graph reset_cache_KEGGemUP retrieve_all_pathways retrieve_kgml subset_kegg_graph

Dependencies:askpass base64enc BiocFileCache BiocGenerics Biostrings bit bit64 blob bslib cachem cli cpp11 crayon curl DBI dbplyr digest dplyr evaluate farver fastmap filelock fontawesome fs generics ggplot2 glue gtable highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lattice lifecycle magrittr Matrix memoise mime openssl pillar pkgconfig png purrr R6 rappdirs RColorBrewer rlang rmarkdown RSQLite S4Vectors S7 sass scales Seqinfo stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun xml2 XVector yaml

The KEGGemUP User's Guide

Edoardo Filippi, Federico Marini

Rendered fromKEGGemUP_userguide.Rmdusingknitr::rmarkdownon Jun 13 2026.

Last update: 2026-06-10
Started: 2026-05-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cleanup the title node from a KEGG igraph object	cleanup_title_node
Create a graph for a KEGG pathway	create_kegg_graph
Return all cached KEGGemUP information	display_cache_KEGGemUP
Export a KEGG graph	export_kegg_graph
Get a KEGG database file	get_kegg_db
Highlight a subset of the KEGG graph	highlight_kegg_graph
Map continuous values to graph nodes	map_results_to_graph
Create an interactive visualization of KEGG pathways with visNetwork	render_kegg_graph
A sample 'data.frame' containing Differential Expression Analysis, generated with 'limma'	res_de_macro_IFNg_vs_naive
Reset all KEGGemUP caches	reset_cache_KEGGemUP
Download all pathways	retrieve_all_pathways
Download a KGML file	retrieve_kgml
Subset a graph object for a KEGG pathway	subset_kegg_graph