BioNet
This is the development version of BioNet; for the stable release version, see BioNet.
Routines for the functional analysis of biological networks
Bioconductor version: Development (3.24)
This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
Author: Marcus Dittrich and Daniela Beisser
Maintainer: Marcus Dittrich <marcus.dittrich at biozentrum.uni-wuerzburg.de>
citation("BioNet")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("BioNet")
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("BioNet")| BioNet Tutorial | R Script | |
| Reference Manual |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software |
| Version | 1.73.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), graph, RBGL |
| Imports | igraph (>= 1.0.1), AnnotationDbi, Biobase |
| System Requirements | |
| URL | http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ |
See More
| Suggests | rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | gatom, SMITE |
| Suggests Me | SANTA, mwcsr |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BioNet_1.73.0.tar.gz |
| Windows Binary (x86_64) | BioNet_1.73.0.zip |
| macOS Binary (big-sur-x86_64) | BioNet_1.73.0.tgz |
| macOS Binary (sonoma-arm64) | BioNet_1.73.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BioNet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BioNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/BioNet/ |
| Package Short Url | https://bioconductor.org/packages/BioNet/ |
| Package Downloads Report | Download Stats |