TFBSTools: an R/bioconductor package for transcription factor binding site analysis - PubMed (original) (raw)

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

Ge Tan et al. Bioinformatics. 2016.

Abstract

: The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation. TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling TFBS profile matrices, scanning sequences and alignments including whole genomes, and querying the JASPAR database. The functionality of the package can be easily extended to include advanced statistical analysis, data visualization and data integration.

Availability and implementation: The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/TFBSTools/).

Contact: ge.tan09@imperial.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

© The Author 2016. Published by Oxford University Press.

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Figures

Fig. 1.

Fig. 1.

A common workflow and classes in TFBSTools. (A) PFMatrix can be converted into PWMatrix, ICMatrix. ICMatrix produces the sequence logos. PWMatrix scans the single sequence or alignment to produce SiteSet object that holds transcription factor binding sites. (B) TFFM: A virtual class for TFFM; TFFMFirst and TFFMDetail are derived from this virtual class. They can produce the position probabilities and the novel graphics representation of TFFM

References

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