DOI: 10.18129/B9.bioc.iNETgrate  

This is the development version of iNETgrate; for the stable release version, see iNETgrate.

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

Bioconductor version: Development (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>

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PDF R Script iNETgrate: Integrating gene expression and DNA methylation data in a gene network
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biocViews BiomedicalInformatics, Classification, Clustering, DNAMethylation, DimensionReduction, GeneExpression, GenePrediction, GraphAndNetwork, KEGG, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, Survival, SystemsBiology, Transcriptomics, mRNAMicroarray
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
Suggests knitr,,, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks(>= 2.29.4)
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