iNETgrate

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 u.washington.edu>

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

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
LinkingTo
Suggests	knitr, org.Hs.eg.db, org.Mm.eg.db, IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi, sesameData, TCGAbiolinks(>= 2.29.4)
SystemRequirements
Enhances
URL
BugReports	https://github.com/Bioconductor/BiocManager/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	iNETgrate_1.1.0.tar.gz
Windows Binary	iNETgrate_1.1.0.zip
macOS Binary (x86_64)	iNETgrate_1.1.0.tgz
macOS Binary (arm64)
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