KEGGlincs
Visualize all edges within a KEGG pathway and overlay LINCS data
Bioconductor version: Release (3.19)
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 "4.4") 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 | ||
NEWS | Text |
Details
biocViews | CellBiology, DataRepresentation, GeneExpression, GraphAndNetwork, KEGG, Network, NetworkInference, Pathways, Software, ThirdPartyClient |
Version | 1.30.0 |
In Bioconductor since | BioC 3.4 (R-3.3) (8 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 |
See More
Suggests | BiocManager (>= 1.20.3), knitr, graph |
Linking To | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | KEGGlincs_1.30.0.tar.gz |
Windows Binary | KEGGlincs_1.30.0.zip (64-bit only) |
macOS Binary (x86_64) | KEGGlincs_1.30.0.tgz |
macOS Binary (arm64) | KEGGlincs_1.30.0.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 |