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iNETgrate

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


Bioconductor version: Release (3.18)

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 u.washington.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("iNETgrate")

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("iNETgrate")
iNETgrate: Integrating gene expression and DNA methylation data in a gene network PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, Classification, Clustering, DNAMethylation, DimensionReduction, GeneExpression, GenePrediction, GraphAndNetwork, KEGG, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, Survival, SystemsBiology, Transcriptomics, mRNAMicroarray
Version 1.0.0
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
System Requirements
URL
Bug Reports https://github.com/Bioconductor/BiocManager/issues
See More
Suggests knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks(>= 2.29.4)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package iNETgrate_1.0.0.tar.gz
Windows Binary iNETgrate_1.0.0.zip
macOS Binary (x86_64) iNETgrate_1.0.0.tgz
macOS Binary (arm64) iNETgrate_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/iNETgrate
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/iNETgrate
Bioc Package Browser https://code.bioconductor.org/browse/iNETgrate/
Package Short Url https://bioconductor.org/packages/iNETgrate/
Package Downloads Report Download Stats