TENET
This is thereleased version of TENET; for the devel version, seeTENET.
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors
Bioconductor version: Release (3.22)
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 DNA 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 tools for visualization and analysis of the results, including plots displaying and comparing methylation and expression data and 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("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 appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TENET")| Using TENET | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics,CellBiology,DNAMethylation,DifferentialExpression,DifferentialMethylation,Epigenetics,FunctionalGenomics,GeneExpression,GeneRegulation,GeneTarget,Genetics,HistoneModification,MethylSeq,MethylationArray,MultipleComparison,RNASeq,Sequencing,Software,Survival,Transcription,Transcriptomics,Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.5) |
| Imports | graphics, grDevices, stats, utils, tools,S4Vectors,GenomicRanges,IRanges, parallel,pastecs,ggplot2 (>= 4.0),RCircos,survival,BSgenome.Hsapiens.UCSC.hg38,seqLogo,Biostrings,matlab,TCGAbiolinks, methods,R.utils,MultiAssayExperiment,SummarizedExperiment,sesame,sesameData,AnnotationHub,ExperimentHub,TENET.ExperimentHub,rtracklayer,MotifDb,BAMMtools,survminer |
| System Requirements | |
| URL | https://github.com/rhielab/TENET |
| Bug Reports | https://github.com/rhielab/TENET/issues |
See More
| Suggests | TENET.AnnotationHub,knitr,rmarkdown,BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | TENET.AnnotationHub,TENET.ExperimentHub |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | TENET_1.2.0.tar.gz |
| Windows Binary (x86_64) | TENET_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | TENET_1.2.0.tgz |
| macOS Binary (arm64) | TENET_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/TENET |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TENET |
| Bioc Package Browser | https://code.bioconductor.org/browse/TENET/ |
| Package Short Url | https://bioconductor.org/packages/TENET/ |
| Package Downloads Report | Download Stats |