KEGGlincs

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see KEGGlincs.

Visualize all edges within a KEGG pathway and overlay LINCS data

Bioconductor version: 3.17

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))
 install.packages("BiocManager")
BiocManager::install("KEGGlincs")

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:

browseVignettes("KEGGlincs")

KEGGlincs Workflows HTML R Script

Reference Manual PDF

NEWS Text

Version 1.26.0

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.

Windows Binary KEGGlincs_1.26.0.zip

macOS Binary (x86_64) KEGGlincs_1.26.0.tgz

macOS Binary (arm64) KEGGlincs_1.26.0.tgz

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

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

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Old Source Packages for BioC 3.17 Source Archive