NCIgraph
This is the released version of NCIgraph; for the devel version, see NCIgraph.
Pathways from the NCI Pathways Database
Bioconductor version: Release (3.23)
Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.
Author: Laurent Jacob
Maintainer: Laurent Jacob <laurent.jacob at gmail.com>
citation("NCIgraph")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NCIgraph")
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("NCIgraph")| NCIgraph: networks from the NCI pathway integrated database as graphNEL objects. | R Script | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Pathways, Software |
| Version | 1.60.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0.0) |
| Imports | graph, KEGGgraph, methods, RBGL, RCy3, R.oo |
| System Requirements | |
| URL |
See More
| Suggests | Rgraphviz |
| Linking To | |
| Enhances | DEGraph |
| Depends On Me | |
| Imports Me | DEGraph |
| Suggests Me | DEGraph |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NCIgraph_1.60.0.tar.gz |
| Windows Binary (x86_64) | NCIgraph_1.60.0.zip |
| macOS Binary (big-sur-x86_64) | NCIgraph_1.60.0.tgz |
| macOS Binary (sonoma-arm64) | NCIgraph_1.60.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NCIgraph |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NCIgraph |
| Bioc Package Browser | https://code.bioconductor.org/browse/NCIgraph/ |
| Package Short Url | https://bioconductor.org/packages/NCIgraph/ |
| Package Downloads Report | Download Stats |