DOI: 10.18129/B9.bioc.enrichTF  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see enrichTF.

Transcription Factors Enrichment Analysis

Bioconductor version: 3.16

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>

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biocViews GeneTarget, GraphAndNetwork, MotifAnnotation, Software, Transcription
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (4 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
Suggests knitr, testthat, webshot
URL https://github.com/wzthu/enrichTF
BugReports https://github.com/wzthu/enrichTF/issues
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