enrichTF

DOI: 10.18129/B9.bioc.enrichTF    

Transcription Factors Enrichment Analysis

Bioconductor version: Release (3.11)

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 (from within R, enter citation("enrichTF")):

Installation

To install this package, start R (version "4.0") 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 1.4.0
In Bioconductor since BioC 3.9 (R-3.6) (1.5 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_1.4.0.tar.gz
Windows Binary enrichTF_1.4.0.zip
macOS 10.13 (High Sierra) enrichTF_1.4.0.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
Old Source Packages for BioC 3.11 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: