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("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 |
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 |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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 | |
| 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/ |
| Package Downloads Report | Download Stats |