To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("NetSAM")
In most cases, you don't need to download the package archive at all.
NetSAM
Network Seriation And Modularization
Bioconductor version: 3.0
The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis.
Author: Jing Wang <jing.wang.2 at vanderbilt.edu>
Maintainer: Bing Zhang <bing.zhang at vanderbilt.edu>
Citation (from within R,
enter citation("NetSAM")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("NetSAM")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("NetSAM")
| R Script | NetSAM | |
| Reference Manual |
Details
| biocViews | Network, Software, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | LGPL |
| Depends | R (>= 2.15.1), methods, igraph (>= 0.6-1), seriation (>= 1.0-6), graph(>= 1.34.0) |
| Imports | methods |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | NetSAM_1.6.0.tar.gz |
| Windows Binary | NetSAM_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | NetSAM_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | NetSAM_1.6.0.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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