KEGGemUP

This is the development version of KEGGemUP; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.24)

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.

Author: Edoardo Filippi [aut] ORCID: 0009-0003-9858-0137 , Myriam Meineck [ctb] ORCID: 0000-0002-3243-2540 , Paul Classen [ctb] ORCID: 0000-0002-9410-0525 , Julia Weinmann-Menke [fnd] ORCID: 0000-0001-7344-8381 , Federico Marini [aut, cre] ORCID: 0000-0003-3252-7758

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("KEGGemUP")):

Edoardo Filippi, Federico Marini. KEGGemUP: Creating, Rendering, and Mapping Omics Data on KEGG Pathway Graphs. doi:10.18129/B9.bioc.KEGGemUP, R package version 0.99.1, https://bioconductor.org/packages/KEGGemUP.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("KEGGemUP")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("KEGGemUP")

The KEGGemUP User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GraphAndNetwork, KEGG, Metabolomics, Network, Pathways, Proteomics, Software, SystemsBiology, Transcriptomics, Visualization
Version	0.99.1
In Bioconductor since	BioC 3.24 (R-4.6)
License	MIT + file LICENSE
Depends	R (>= 4.5.0)
Imports	BiocFileCache, httr2, ggplot2, rlang, methods, igraph, scales, KEGGREST, visNetwork, RColorBrewer, htmlwidgets, xml2, grDevices, stats, tools, utils
System Requirements
URL	https://github.com/imbeimainz/KEGGemUP
Bug Reports	https://github.com/imbeimainz/KEGGemUP/issues

Suggests	knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	KEGGemUP_0.99.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)	KEGGemUP_0.99.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/KEGGemUP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/KEGGemUP
Package Short Url	https://bioconductor.org/packages/KEGGemUP/
Package Downloads Report	Download Stats