To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("coexnet")

In most cases, you don't need to download the package archive at all.

coexnet

DOI: 10.18129/B9.bioc.coexnet    

This is the development version of coexnet; to use it, please install the devel version of Bioconductor.

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

Bioconductor version: Development (3.6)

Extracts the gene expression matrix from GEO DataSets (.CEL files) as a AffyBatch object. Additionally, can make the normalization process using two different methods (vsn and rma). The summarization (pass from multi-probe to one gene) uses two different criteria (Maximum value and Median of the samples expression data) and the process of gene differentially expressed analisys using two methods (sam and acde). The construction of the co-expression network can be conduced using two different methods, Pearson Correlation Coefficient (PCC) or Mutual Information (MI) and choosing a threshold value using a graph theory approach.

Author: Juan David Henao [aut,cre], Liliana Lopez-Kleine [aut], Andres Pinzon-Velasco [aut]

Maintainer: Juan David Henao <judhenaosa at unal.edu.co>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("coexnet")

Documentation

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

browseVignettes("coexnet")

 

PDF R Script The title
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkInference, Normalization, Software, SystemsBiology
Version 0.99.21
In Bioconductor since BioC 3.6 (R-3.4)
License LGPL
Depends R (>= 3.4)
Imports affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown
LinkingTo
Suggests RUnit, BiocGenerics, knitr
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.

Source Package coexnet_0.99.21.tar.gz
Windows Binary coexnet_0.99.21.zip
Mac OS X 10.11 (El Capitan) coexnet_0.99.21.tgz
Source Repository git clone https://git.bioconductor.org/packages/coexnet
Package Short Url http://bioconductor.org/packages/coexnet/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: