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netboxr

netboxr

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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

Reference Manual PDF

Details

biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.11.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 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
Linking To
Suggests paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, cgdsr
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64) netboxr_1.11.0.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/
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