This is the released version of TENET; for the devel version, see TENET.
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factorsBioconductor version: Release (3.21)
TENET identifies key transcription factors (TFs) and regulatory elements (REs) linked to a specific cell type by finding significantly correlated differences in gene expression and RE methylation between case and control input datasets, and identifying the top genes by number of significant RE DNA methylation site links. It also includes many additional tools to aid in visualization and analysis of the results, including plots displaying and comparing methylation and expression data and RE DNA methylation site link counts, survival analysis, TF motif searching in the vicinity of linked RE DNA methylation sites, custom TAD and peak overlap analysis, and UCSC Genome Browser track file generation. A utility function is also provided to download methylation, expression, and patient survival data from The Cancer Genome Atlas (TCGA) for use in TENET or other analyses.
Author: Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut] ORCID: 0000-0002-7639-0549 , Zexun Wu [aut] ORCID: 0000-0003-2566-1326 , Ethan Nelson-Moore [aut] ORCID: 0009-0001-6903-9232 , Suhn Rhie [aut] ORCID: 0000-0002-5522-5296
Maintainer: Rhie Lab at the University of Southern California <rhielab at gmail.com>
Citation (from within R, entercitation("TENET")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TENET")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TENET")Follow Installation instructions to use this package in your R session.
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