NetSAM

DOI: 10.18129/B9.bioc.NetSAM    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see NetSAM.

Network Seriation And Modularization

Bioconductor version: 3.13

The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a weighted or unweighted 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. The NetSAM package can also generate correlation network (e.g. co-expression network) based on the input matrix data, perform seriation and modularization analysis for the correlation network and calculate the associations between the sample features and modules or identify the associated GO terms for the modules.

Author: Jing Wang <jing.wang at bcm.edu>

Maintainer: Zhiao Shi <zhiao.shi at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NetSAM")

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("NetSAM")

 

PDF	R Script	NetSAM User Guide
PDF		Reference Manual

Details

biocViews	Software
Version	1.32.0
In Bioconductor since	BioC 2.13 (R-3.0) (8 years)
License	LGPL
Depends	R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 0.6-1), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt(>= 2.18.0)
Imports	methods, AnnotationDbi(>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), survival (>= 2.37-7), GO.db(>= 2.10.0), R2HTML (>= 2.2.0), DBI (>= 0.5-1)
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Suggests	RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr, markdown
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Build Report

Package Archives

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

Source Package	NetSAM_1.32.0.tar.gz
Windows Binary	NetSAM_1.31.0.zip
macOS 10.13 (High Sierra)	NetSAM_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NetSAM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NetSAM
Package Short Url	https://bioconductor.org/packages/NetSAM/
Package Downloads Report	Download Stats