###Code From the Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

In an effort to make my results reproducible and aid others in their own data analysis, I've included all of the code used in the paper. I hope this will be useful and feel free to conact me with suggestions/comments/questions. Happy data mining!

-Alex

Notebook 1: Library Statistics
Notebook 2: Splice Site Analysis
Notebook 3: Splicing Frame and Nonsense Mediated Decay Analysis
Notebook 4: Estimating Motif Effects
Notebook 5: Combinatorial Motif Effects
Notebook 6: Learning Curves for Models Predicting Alt. 5SS Usage
Notebook 7: A Model of Alternative 5\prime Splicing
Notebook 8: Predictions on Alt. 5SS Events in the Genome
Notebook 9: Training a Joint Model with Both the Alt. 5SS and Alt. 3SS Libraries
Notebook 10: Predicting the Effects of SNPs on Alternative 5\prime Splicing
Notebook 11: Predicting the Effects of SNPs on Exon Skipping