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 (from within R, enter 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 PDF
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
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Suggests paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr
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Imports Me
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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