KEGGlincs
Visualize all edges within a KEGG pathway and overlay LINCS data
Bioconductor version: Release (3.20)
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 | 1.32.0 |
| 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 | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | KEGGlincs_1.32.0.tar.gz |
| Windows Binary (x86_64) | KEGGlincs_1.32.0.zip |
| macOS Binary (x86_64) | KEGGlincs_1.32.0.tgz |
| macOS Binary (arm64) | KEGGlincs_1.32.0.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 |