Code and Data
Code
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auto_peak_call.ipynb | Finds regions that have a signficant effect on gene expression.
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SortSeq_Information_Footprints.ipynb | Tutorial script which plots information footprints.
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plot_informationfootprint.py | Script which plots information footprints.
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find_all_regions.ipynb | Combines the output of the auto_peak_call.ipynb into potential transcription factor binding sites.
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peak_utils.py | Support functions for the auto_peak_call.ipynb notebook.
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software.tar.gz | All code files with associated data files in the right directory structure.
Data Sets
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MCMC inference of expression shift for all genes in the paper. | (filetype: .zip)(2 gb)
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Datasets used to generate all figures in the paper. | (filetype: .zip)(100 mb)
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The datasets to use with the tutorial notebooks. Download and extract this folder to use the notebooks. | (filetype: .zip)(100 mb)