Deepcpg

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](http://deepcpg.readthedocs.io/en/latest/scripts/index.htmlmodule-scripts.dcpg_eval_perf) and R markdown files for computing and visualizing performance metrics genome-wide and in annotated contexts.
* Adds [dcpg_snp.py](http://deepcpg.readthedocs.io/en/latest/scripts/index.htmlmodule-scripts.dcpg_snp) for computing mutation effects.
* Adds [notebooks](https://github.com/cangermueller/deepcpg/tree/master/examples) on computing mutation effects and predicting inter-cell statistics.
* Adds documentation of [DeepCpG scripts](http://deepcpg.readthedocs.io/latest/scripts/index.html).
* 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](http://deepcpg.readthedocs.io/en/latest/data.htmldata) about creating and analyzing Data.
+ Updates documentation of [scripts](http://deepcpg.readthedocs.io/en/latest/scripts/index.htmlscripts) and [library](http://deepcpg.readthedocs.io/en/latest/lib/index.htmllibrary).

Source code as used in the manuscript.