Abstract—Although there has been substantial research in software analytics for effort estimation in traditional software projects, little work has been done for estimation in agile projects, especially estimating user stories or issues. Story points are the most common unit of measure used for estimating the effort involved in implementing a user story or resolving an issue. In this paper, we offer for the first time a comprehensive dataset for story points-based estimation that contains 23,313 issues from 16 open source projects. We also propose a prediction model for estimating story points based on a novel combination of two powerful deep learning architectures: long short-term memory and recurrent highway network. Our prediction system is endto- end trainable from raw input data to prediction outcomes without any manual feature engineering. An empirical evaluation demonstrates that our approach consistently outperforms three common effort estimation baselines and two alternatives in both Mean Absolute Error and the Standardized Accuracy.