enrichTF
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see enrichTF.
Transcription Factors Enrichment Analysis
Bioconductor version: 3.19
As transcription factors (TFs) play a crucial role in regulating the transcription process through binding on the genome alone or in a combinatorial manner, TF enrichment analysis is an efficient and important procedure to locate the candidate functional TFs from a set of experimentally defined regulatory regions. While it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.
Author: Zheng Wei, Zhana Duren, Shining Ma
Maintainer: Zheng Wei <wzwz at stanford.edu>
citation("enrichTF")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("enrichTF")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | GeneTarget, GraphAndNetwork, MotifAnnotation, Software, Transcription |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL-3 |
| Depends | pipeFrame |
| Imports | BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils, methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges, BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr, heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices, magrittr |
| System Requirements | |
| URL | https://github.com/wzthu/enrichTF |
| Bug Reports | https://github.com/wzthu/enrichTF/issues |
See More
| Suggests | knitr, testthat, webshot |
| 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 | |
| Windows Binary (x86_64) | enrichTF_1.20.0.zip |
| macOS Binary (x86_64) | enrichTF_1.20.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/enrichTF |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/enrichTF |
| Package Short Url | https://bioconductor.org/packages/enrichTF/ |
| Package Downloads Report | Download Stats |