To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BioNet")
In most cases, you don't need to download the package archive at all.
BioNet
Routines for the functional analysis of biological networks
Bioconductor version: 3.0
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 (from within R,
enter citation("BioNet")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("BioNet")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BioNet")
| R Script | BioNet Tutorial | |
| Reference Manual |
Details
| biocViews | DataImport, DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software |
| Version | 1.26.1 |
| In Bioconductor since | BioC 2.7 (R-2.12) |
| License | GPL (>= 2) |
| Depends | R (>= 2.10.0), Biobase, graph, RBGL |
| Imports | igraph (>= 0.7), AnnotationDbi |
| LinkingTo | |
| Suggests | rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML |
| SystemRequirements | |
| Enhances | |
| URL | http://bionet.bioapps.biozentrum.uni-wuerzburg.de/ |
| Depends On Me | |
| Imports Me | HTSanalyzeR |
| Suggests Me | SANTA |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | BioNet_1.26.1.tar.gz |
| Windows Binary | BioNet_1.26.1.zip |
| Mac OS X 10.6 (Snow Leopard) | BioNet_1.26.1.tgz |
| Mac OS X 10.9 (Mavericks) | BioNet_1.26.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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