Adds support for Keras >2.2.0 and fixes minor bugs.

• Add support for Keras 2.1.4 and Tensorflow 1.5.0.
• Minor bug-fixes.

Uses Keras 2 as main Keras version.

Adds evaluation scripts and notebooks, improves documentation, and fixes minor bugs.

• Adds dcpg_eval_perf.py and R markdown files for computing and visualizing performance metrics genome-wide and in annotated contexts.
• Adds dcpg_snp.py for computing mutation effects.
• Adds notebooks on computing mutation effects and predicting inter-cell statistics.
• Adds documentation of DeepCpG scripts.
• Adds integration tests.
• Includes minor bug-fixes.

Extends dcpg_data.py, updates documentation, and fixes minor bugs.

• Extends dcpg_data.py to support bedGraph and TSV input files.
• Enables training on continuous methylation states.
• Adds documentation about creating and analyzing Data.
• Updates documentation of scripts and library.

Source code as used in the manuscript.