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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

Bioconductor version: Development (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")):

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews CellBiology, DataRepresentation, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkInference, Pathways, Software, ThirdPartyClient
Version 1.27.0
In Bioconductor since BioC 3.4 (R-3.3) (7 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
Linking To
Suggests BiocManager (>= 1.20.3), knitr, graph
System Requirements Cytoscape (>= 3.3.0), Java (>= 8)
Enhances
URL
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Depends On Me
Imports Me
Suggests Me
Links To Me
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Package Archives

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

Source Package KEGGlincs_1.27.0.tar.gz
Windows Binary KEGGlincs_1.27.0.zip
macOS Binary (x86_64) KEGGlincs_1.27.0.tgz
macOS Binary (arm64) KEGGlincs_1.27.0.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/
Package Downloads Report Download Stats