enrichTF

DOI: 10.18129/B9.bioc.enrichTF    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see enrichTF.

Transcription Factors Enrichment Analysis

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	An Introduction to enrichTF
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneTarget, GraphAndNetwork, MotifAnnotation, Software, Transcription
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 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
LinkingTo
Suggests	knitr, testthat, webshot
SystemRequirements
Enhances
URL	https://github.com/wzthu/enrichTF
BugReports	https://github.com/wzthu/enrichTF/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	enrichTF_1.8.0.tar.gz
Windows Binary	enrichTF_1.8.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	enrichTF_1.8.0.tgz
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