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Bioinformatics. 2016 May 15;32(10):1555-6. doi: 10.1093/bioinformatics/btw024. Epub 2016 Jan 21.

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

Author information

1
Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK.

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.

PMID:
26794315
PMCID:
PMC4866524
DOI:
10.1093/bioinformatics/btw024
[Indexed for MEDLINE]
Free PMC Article

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