coexnet

DOI: 10.18129/B9.bioc.coexnet  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see coexnet.

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

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("coexnet")

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("coexnet")

 

PDF	R Script	The title
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkInference, Normalization, Software, SystemsBiology
Version	1.19.1
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	LGPL
Depends	R (>= 3.6)
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
Links To Me
Build Report

Package Archives

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

Source Package	coexnet_1.19.1.tar.gz
Windows Binary	coexnet_1.19.1.zip
macOS Binary (x86_64)	coexnet_1.19.1.tgz
macOS Binary (arm64)	coexnet_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/coexnet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/coexnet
Package Short Url	https://bioconductor.org/packages/coexnet/
Package Downloads Report	Download Stats