netboxr

DOI: 10.18129/B9.bioc.netboxr  

netboxr

Bioconductor version: Release (3.16)

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], Chris Sander [aut]

Maintainer: Eirc Minwei Liu <emliu.research at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	NetBoxR Tutorial
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version	1.9.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 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
LinkingTo
Suggests	paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	netboxr_1.9.0.tar.gz
Windows Binary	netboxr_1.9.0.zip
macOS Binary (x86_64)	netboxr_1.9.0.tgz
macOS Binary (arm64)	netboxr_1.10.0.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