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Bioconductor - NetSAM

NetSAM

This is the released version of NetSAM; for the devel version, see NetSAM.

Network Seriation And Modularization

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("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")
Details biocViews Software Version 1.48.0 In Bioconductor since BioC 2.13 (R-3.0) (11.5 years) License LGPL Depends R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), 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) System Requirements URL See More 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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