netboxr

DOI: 10.18129/B9.bioc.netboxr    

This is the development version of netboxr; for the stable release version, see netboxr.

netboxr

Bioconductor version: Development (3.12)

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 (from within R, enter citation("netboxr")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.7
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.1.7.tar.gz
Windows Binary netboxr_1.1.7.zip
macOS 10.13 (High Sierra) netboxr_1.1.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/netboxr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/netboxr
Package Short Url https://bioconductor.org/packages/netboxr/
Package Downloads Report Download Stats

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