ggkegg

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see ggkegg.

Analyzing and visualizing KEGG information using the grammar of graphics

Bioconductor version: 3.19

This package aims to import, parse, and analyze KEGG data such as KEGG PATHWAY and KEGG MODULE. The package supports visualizing KEGG information using ggplot2 and ggraph through using the grammar of graphics. The package enables the direct visualization of the results from various omics analysis packages.

Author: Noriaki Sato [cre, aut]

Maintainer: Noriaki Sato <nori at hgc.jp>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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("ggkegg")

ggkegg HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, KEGG, Pathways, Software

Version 1.2.3

In Bioconductor since BioC 3.18 (R-4.3) (1 year)

License MIT + file LICENSE

Depends R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph

Imports BiocFileCache, GetoptLong, data.table, dplyr, magick, patchwork, shadowtext, stringr, tibble, org.Hs.eg.db, methods, utils, stats, AnnotationDbi, grDevices, gtable

System Requirements

URL https://github.com/noriakis/ggkegg

Bug Reports https://github.com/noriakis/ggkegg/issues

Suggests knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me pathfindR

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package ggkegg_1.2.3.tar.gz

Windows Binary (x86_64) ggkegg_1.2.3.zip

macOS Binary (x86_64) ggkegg_1.2.3.tgz

macOS Binary (arm64) ggkegg_1.2.3.tgz

Source Repository git clone https://git.bioconductor.org/packages/ggkegg

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggkegg

Bioc Package Browser https://code.bioconductor.org/browse/ggkegg/

Package Short Url https://bioconductor.org/packages/ggkegg/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.19 Source Archive