KEGGlincs

This is the released version of KEGGlincs; for the devel version, see KEGGlincs.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Visualize all edges within a KEGG pathway and overlay LINCS data

Bioconductor version: Release (3.23)

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")):

Shana White. KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data. doi:10.18129/B9.bioc.KEGGlincs, R package version 1.38.0, https://bioconductor.org/packages/KEGGlincs.

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")

BiocManager::install("KEGGlincs")

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("KEGGlincs")

KEGGlincs Workflows	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellBiology, DataRepresentation, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkInference, Pathways, Software, ThirdPartyClient
Version	1.38.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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)
URL

Suggests	BiocManager (>= 1.20.3), knitr, graph
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	KEGGlincs_1.38.0.tar.gz
Windows Binary (x86_64)	KEGGlincs_1.38.0.zip
macOS Binary (big-sur-x86_64)	KEGGlincs_1.38.0.tgz
macOS Binary (sonoma-arm64)	KEGGlincs_1.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/KEGGlincs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/KEGGlincs
Package Short Url	https://bioconductor.org/packages/KEGGlincs/
Package Downloads Report	Download Stats