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Transcriptional regulatory network (TRN) structures document the influence of regulatory proteins called transcription factors (TFs) on their associated target genes (TGs). TRN models were initially established for well-studied models such as Escherichia coli, but their application is broadening through improved computational inference and the availability of experimental data, allowing the identification of strain-specific differences in regulation. Such investigations require simultaneous displays of multiple networks that current network visualisation tools cannot support. TRNDiff, a javascript application built on top of D3.js, uses a simple wagon wheel metaphor for each network, allowing rapid visualisation and comparison at considerable scale, allowing hundreds of individuals to be seen on suitable displays. TRNDiff supports functional highlighting, Boolean operations and link selection. The tool is released under an Apache open source licence.

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