DESCRIPTION

Package: coexnet
Type: Package
Title: coexnet: An R package to build CO-EXpression NETworks from Microarray Data
Version: 0.99.21
Author: Juan David Henao [aut,cre], Liliana Lopez-Kleine [aut], Andres Pinzon-Velasco [aut]
Maintainer: Juan David Henao <judhenaosa@unal.edu.co>
Description: 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.
License: LGPL
LazyData: TRUE
Depends:
    R (>= 3.4)
Imports:
    affy,
    siggenes,
    GEOquery,
    vsn,
    igraph,
    acde,
    Biobase,
    limma,
    graphics,
    stats,
    utils,
    STRINGdb,
    SummarizedExperiment,
    minet,
    rmarkdown
Suggests: 
    RUnit, 
    BiocGenerics,
    knitr
VignetteBuilder: knitr
biocViews: GeneExpression, Microarray, DifferentialExpression, GraphAndNetwork, 
    NetworkInference, SystemsBiology, Normalization, Network
RoxygenNote: 6.0.1