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Integrates DNA methylation data with gene expression in a single gene network

Bioconductor version: Release (3.19)

The iNETgrate package provides functions to build a correlation network in which nodes are genes. DNA methylation and gene expression data are integrated to define the connections between genes. This network is used to identify modules (clusters) of genes. The biological information in each of the resulting modules is represented by an eigengene. These biological signatures can be used as features e.g., for classification of patients into risk categories. The resulting biological signatures are very robust and give a holistic view of the underlying molecular changes.

Author: Isha Mehta [aut] , Ghazal Ebrahimi [aut], Hanie Samimi [aut], Habil Zare [aut, cre]

Maintainer: Habil Zare <zare at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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

iNETgrate: Integrating gene expression and DNA methylation data in a gene network PDF R Script
Reference Manual PDF


biocViews BiomedicalInformatics, Classification, Clustering, DNAMethylation, DimensionReduction, GeneExpression, GenePrediction, GraphAndNetwork, KEGG, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, Survival, SystemsBiology, Transcriptomics, mRNAMicroarray
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3
Depends R (>= 4.3.0), BiocStyle(>= 2.18.1)
Imports SummarizedExperiment, GenomicRanges(>= 1.24.1), stats, WGCNA, grDevices, graphics, survival, igraph, Pigengene(>= 1.19.26), Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast, tidyr, tidyselect, utils
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Suggests knitr,,, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks(>= 2.29.4)
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Source Package iNETgrate_1.2.0.tar.gz
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