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bioRxiv · 10.1101/036053

RTFBSDB: an integrated framework for transcription factor binding site analysis

Zhong Wang·Andre L Martins·Charles G Danko
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Abstract

Transcription factors (TFs) regulate complex programs of gene transcription by binding to short DNA sequence motifs. Here we introduce rtfbsdb, a unified framework that integrates a database of more than 65,000 TF binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters motifs with similar DNA sequence specificities and optionally integrates RNA-seq or PRO-seq data to restrict analyses to motifs recognized by TFs expressed in the cell type of interest. Our package allows common analyses to be performed rapidly in an integrated environment.\n\nAvailability: rtfbsdb is available via github (https://github.com/Danko-Lab/rtfbsdb).

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Zhong Wang, Andre L Martins, Charles G Danko. 2016-01-06. RTFBSDB: an integrated framework for transcription factor binding site analysis. https://doi.org/10.1101/036053

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