TENET
R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors
Bioconductor version: 3.23 · Package version: 1.4.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TENET")Details
| Maintainer | Rhie Lab at the University of Southern California <rhielab@gmail.com> |
| Author | Rhie Lab at the University of Southern California [cre], Daniel Mullen [aut] (ORCID: <https://orcid.org/0000-0002-7639-0549>), Zexun Wu [aut] (ORCID: <https://orcid.org/0000-0003-2566-1326>), Ethan Nelson-Moore [aut] (ORCID: <https://orcid.org/0009-0001-6903-9232>), Suhn Rhie [aut] (ORCID: <https://orcid.org/0000-0002-5522-5296>) |
| License | GPL-2 |
| URL | https://github.com/rhielab/TENET |
| Bug Reports | https://github.com/rhielab/TENET/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiomedicalInformatics, CellBiology, DNAMethylation, DifferentialExpression, DifferentialMethylation, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, GeneTarget, Genetics, HistoneModification, MethylSeq, MethylationArray, MultipleComparison, RNASeq, Sequencing, Software, Survival, Transcription, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/TENET/ |
Citation
From within R, enter citation("TENET"):
Daniel Mullen, Zexun Wu, Ethan Nelson-Moore, Suhn Rhie. TENET: R package for TENET (Tracing regulatory Element Networks using Epigenetic Traits) to identify key transcription factors. doi:10.18129/B9.bioc.TENET, R package version 1.4.0, https://bioconductor.org/packages/TENET.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TENET_1.4.0.tar.gz |
| Windows binary (x86_64) | TENET_1.4.0.zip |
| macOS binary (arm64) | TENET_1.4.0.tgz |
| macOS binary (x86_64) | TENET_1.4.0.tgz |
Dependencies
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
Suggests: TENET.AnnotationHub, knitr, rmarkdown, BiocStyle
Reverse dependencies
Suggests Me (2): TENET.AnnotationHub, TENET.ExperimentHub