enrichTF
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see enrichTF.
Transcription Factors Enrichment Analysis
Bioconductor version: 3.10
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 "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("enrichTF")| An Introduction to enrichTF | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneTarget, GraphAndNetwork, MotifAnnotation, Software, Transcription |
| Version | 1.2.3 |
| In Bioconductor since | BioC 3.9 (R-3.6) (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 | enrichTF_1.2.3.tar.gz |
| Windows Binary | enrichTF_1.2.3.zip |
| Mac OS X 10.11 (El Capitan) | enrichTF_1.2.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/enrichTF |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/enrichTF |
| Bioc Package Browser | https://code.bioconductor.org/browse/enrichTF/ |
| Package Short Url | https://bioconductor.org/packages/enrichTF/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |