NetSAM
This is the development version of NetSAM; for the stable release version, see NetSAM.
Network Seriation And Modularization
Bioconductor version: Development (3.24)
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("NetSAM")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| NetSAM User Guide | R Script | |
| Reference Manual |
Details
| biocViews | Software |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (13 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.
| Source Package | NetSAM_1.53.0.tar.gz |
| Windows Binary (x86_64) | NetSAM_1.53.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | NetSAM_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | NetSAM_1.53.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |