coexnet
This package is for version 3.8 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: 3.8
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("coexnet")):
Installation
To install this package, start R (version "3.5") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkInference, Normalization, Software, SystemsBiology |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | LGPL |
| Depends | R (>= 3.4) |
| Imports | affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma, graphics, stats, utils, STRINGdb, SummarizedExperiment, minet, rmarkdown |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr |
| 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 | coexnet_1.4.0.tar.gz |
| Windows Binary | coexnet_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | coexnet_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/coexnet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/coexnet |
| Bioc Package Browser | https://code.bioconductor.org/browse/coexnet/ |
| Package Short Url | https://bioconductor.org/packages/coexnet/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |