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enrichTF

Transcription Factors Enrichment Analysis


Bioconductor version: Release (3.18)

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 "4.3") 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 PDF
NEWS Text

Details

biocViews GeneTarget, GraphAndNetwork, MotifAnnotation, Software, Transcription
Version 1.18.0
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
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Suggests knitr, testthat, webshot
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Package Archives

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

Source Package enrichTF_1.18.0.tar.gz
Windows Binary enrichTF_1.18.0.zip
macOS Binary (x86_64) enrichTF_1.18.0.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
Bioc Package Browser https://code.bioconductor.org/browse/enrichTF/
Package Short Url https://bioconductor.org/packages/enrichTF/
Package Downloads Report Download Stats