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 (3.20)
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("iNETgrate")):
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")| iNETgrate: Integrating gene expression and DNA methylation data in a gene network | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Classification, Clustering, DNAMethylation, DimensionReduction, GeneExpression, GenePrediction, GraphAndNetwork, KEGG, Network, NetworkInference, Normalization, PrincipalComponent, RNASeq, Software, Survival, SystemsBiology, Transcriptomics, mRNAMicroarray |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iNETgrate_1.3.0.tar.gz |
| Windows Binary (x86_64) | iNETgrate_1.3.0.zip (64-bit only) |
| macOS Binary (x86_64) | iNETgrate_1.3.0.tgz |
| macOS Binary (arm64) | iNETgrate_1.3.0.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 |