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>

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

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")
The title PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkInference, Normalization, Software, SystemsBiology
Version 1.19.1
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License LGPL
Depends R (>= 3.6)
Imports affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown
System Requirements
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Suggests RUnit, BiocGenerics, knitr
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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
Old Source Packages for BioC 3.16 Source Archive