DNAshapedTFBS_notebooks

This directory contains the data and IPython notebooks used to generate the figures in our manuscript DNA shape features improve transcription factor binding site predictions in vivo (Mathelier et al., 2016, under review).

Notebooks

• E2F_combined.ipynb: Used to generate plots for Figures 5A and S3A.
• EncodeDinucMatched1st2ndDnashapeDimo.ipynb: Used to generate plots for Figures in Data S3 and S7.
• EncodeGCmatched1st2ndDNAshapeDimo.ipynb: Used to generate plots for Figures 2, 4, and Figures in Data S2, S6, and S7. Used to generate Table S2 in Data S1.
• EncodeReccurentPeaksGCmatched1st2ndDNAshapeDimo.ipynb: Used to generate plots for Figures in Data S4.
• EncodeGCmatched1st2ndDNAshapeDimoMethodsComparisons.ipynb: Used to generate plots for Figure 3 and Figures in Data S5.
• MADS_combined.ipynb: Used to generate plots for Figures 5B, 7A and S3B.
• PlantsGCmatched1st2ndDNAshapeDimo.ipynb: Used to generate Figures in Data S7.
• PlantsDinucMatched1st2ndDNAshapeDimo.ipynb: Used to generate Figures in Data S7.

Launching the notebooks

We recommend to use binder to launch the multiple IPython notebooks: