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This is the development version of NetSAM; for the stable release version, see NetSAM.

Network Seriation And Modularization

Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("NetSAM")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

NetSAM User Guide PDF R Script
Reference Manual PDF


biocViews Software
Version 1.43.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 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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Package Archives

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

Source Package NetSAM_1.43.0.tar.gz
Windows Binary NetSAM_1.43.0.zip
macOS Binary (x86_64) NetSAM_1.43.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/NetSAM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NetSAM
Bioc Package Browser https://code.bioconductor.org/browse/NetSAM/
Package Short Url https://bioconductor.org/packages/NetSAM/
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