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README

This repository contains the analysis code for our Nature Biotechnology manuscript: ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

If you are interested in running this code to reproduce our analysis, we recommend you use our pre-configured Amazon Machine Image (AMI). The image has appropriate versions of all required software and includes the raw and processed data files. You can find more information about the AMI at http://research.stowers.org/zeitlingerlab/data.

The setup instructions used to configure the AMI are also available in this repository:

Amazon EC2 AMI setup notes

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Analysis code for our ChIP-nexus Nature Biotechnology manuscript

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