netboxr
This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see netboxr.
netboxr
Bioconductor version: 3.13
NetBox is a network-based approach that combines prior knowledge with a network clustering algorithm. The algorithm allows for the identification of functional modules and allows for combining multiple data types, such as mutations and copy number alterations. NetBox performs network analysis on human interaction networks, and comes pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Author: Eric Minwei Liu [aut,cre], Augustin Luna [aut], Ethan Cerami [aut]
Maintainer: Eirc Minwei Liu <emliu.research at gmail.com>
citation("netboxr")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("netboxr")
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("netboxr")| NetBoxR Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
| License | LGPL-3 + file LICENSE |
| Depends | R (>= 4.0.0), igraph (>= 1.2.4.1), parallel |
| Imports | RColorBrewer, DT, stats, clusterProfiler, data.table, gplots, jsonlite, plyr |
| System Requirements | |
| URL |
See More
| Suggests | paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr |
| 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 | netboxr_1.4.0.tar.gz |
| Windows Binary | netboxr_1.4.0.zip |
| macOS 10.13 (High Sierra) | netboxr_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/netboxr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/netboxr |
| Bioc Package Browser | https://code.bioconductor.org/browse/netboxr/ |
| Package Short Url | https://bioconductor.org/packages/netboxr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |