Software

NRLB

Our Java program “NRLB” for constructing highly accurate feature-based biophysical protein-DNA interaction models directly from high-throughput data is available on GitHub. For a detailed description of the underlying method, see Rastogi et al., PNAS 2018.

SELEX

Our R package “SELEX” for analyzing high-throughput protein-DNA interaction data is available on Bioconductor.org. For a detailed description of the underlying methods, see Slattery et al., Cell 2011 and Riley et al., 2015

REDUCE Suite

Using the latest version of our REDUCE Suite you can perform integrative analysis of sequence and expression data. It provides an integrated set of tools for motif discovery (“MatrixREDUCE”), inferring motif activities (“Transfactivity”), and generating sequence logos (“LogoGenerator”), including the “affinity/energy logos” that our lab invented. The software is available by registering on our new REDUCE Forum.

DSSR

DSSR is a new integrated software tool for dissecting the spatial structure of RNA that was developed by Xiang-Jun Lu, an Research Scientist in our lab who created the widely used 3DNA software.