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Visualize all edges within a KEGG pathway and overlay LINCS data

Bioconductor version: Release (3.18)

See what is going on 'under the hood' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.

Author: Shana White

Maintainer: Shana White <vandersm at mail.uc.edu>, Mario Medvedovic <medvedm at ucmail.uc.edu>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

KEGGlincs Workflows HTML R Script
Reference Manual PDF


biocViews CellBiology, DataRepresentation, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkInference, Pathways, Software, ThirdPartyClient
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.3), KOdata, hgu133a.db, org.Hs.eg.db(>= 3.3.0)
Imports AnnotationDbi, KEGGgraph, igraph, plyr, gtools, httr, RJSONIO, KEGGREST, methods, graphics, stats, utils, XML, grDevices
System Requirements Cytoscape (>= 3.3.0), Java (>= 8)
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Suggests BiocManager (>= 1.20.3), knitr, graph
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Follow Installation instructions to use this package in your R session.

Source Package KEGGlincs_1.28.0.tar.gz
Windows Binary KEGGlincs_1.28.0.zip
macOS Binary (x86_64) KEGGlincs_1.28.0.tgz
macOS Binary (arm64) KEGGlincs_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/KEGGlincs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/KEGGlincs
Bioc Package Browser https://code.bioconductor.org/browse/KEGGlincs/
Package Short Url https://bioconductor.org/packages/KEGGlincs/
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