KEGGlincs

DOI: 10.18129/B9.bioc.KEGGlincs    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see KEGGlincs.

Visualize all edges within a KEGG pathway and overlay LINCS data [option]

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	KEGGlincs Workflows
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBiology, DataRepresentation, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkInference, Pathways, Software, ThirdPartyClient
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 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
LinkingTo
Suggests	BiocManager (>= 1.20.3), knitr, graph
SystemRequirements	Cytoscape (>= 3.3.0), Java (>= 8)
Enhances
URL
Depends On Me
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Suggests Me
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Build Report

Package Archives

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

Source Package	KEGGlincs_1.8.0.tar.gz
Windows Binary	KEGGlincs_1.8.0.zip
Mac OS X 10.11 (El Capitan)	KEGGlincs_1.8.0.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	http://bioconductor.org/packages/KEGGlincs/
Package Downloads Report	Download Stats