KEGGlincs

DOI: 10.18129/B9.bioc.KEGGlincs    

This is the development version of KEGGlincs; for the stable release version, see KEGGlincs.

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

Bioconductor version: Development (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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("KEGGlincs", version = "devel")

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 1.7.3
In Bioconductor since BioC 3.4 (R-3.3) (2 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
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package KEGGlincs_1.7.3.tar.gz
Windows Binary KEGGlincs_1.7.3.zip
Mac OS X 10.11 (El Capitan) KEGGlincs_1.7.3.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/
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