TFBSTools

TFBSTools is a comprehensive R/Bioconductor package designed to analyze and manipulate transcription factor binding sites (TFBSs) and their profile matrices across genomes, facilitating computational studies of gene regulation. It offers a robust set of tools for working with TFBS profile matrices, scanning sequences and alignments—including whole genomes—and querying the JASPAR database for transcription factor profiles. The package supports various functionalities that users can expand to incorporate advanced statistical analyses, data visualization, and integration.

Topic

Transcription factors and regulatory sites

Detail

  • Operation: Sequence motif recognition;Transcription factor binding site prediction;Transcriptional regulatory element prediction

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.40.0

  • Credit: EU FP7 and Medical Research Council UK.

  • Input: Nucleic acid sequence record [Textual format]

  • Output: Plot [Image format]

  • Contact: Ge Tan ge_tan@live.com

  • Collection: -

  • Maturity: Stable

Publications

  • TFBSTools: an R/bioconductor package for transcription factor binding site analysis.
  • Tan G and Lenhard B. TFBSTools: an R/bioconductor package for transcription factor binding site analysis. TFBSTools: an R/bioconductor package for transcription factor binding site analysis. 2016; 32:1555-6. doi: 10.1093/bioinformatics/btw024
  • https://doi.org/10.1093/bioinformatics/btw024
  • PMID: 26794315
  • PMC: PMC4866524

Download and documentation

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