Skip to content

Commit c6f178c

Browse files
cangermuellercangermueller
committed
Update documentation
1 parent efa0ee2 commit c6f178c

File tree

10 files changed

+101
-76
lines changed

10 files changed

+101
-76
lines changed

‎LICENSE

+16-23
Original file line numberDiff line numberDiff line change
@@ -1,26 +1,19 @@
1-
Copyright (c) 2017, Christof Angermueller
2-
All rights reserved.
1+
Copyright (c) 2017 Christof Angermueller
32

4-
Redistribution and use in source and binary forms, with or without
5-
modification, are permitted provided that the following conditions are met:
3+
Permission is hereby granted, free of charge, to any person obtaining a copy
4+
of this software and associated documentation files (the "Software"), to deal
5+
in the Software without restriction, including without limitation the rights
6+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
7+
copies of the Software, and to permit persons to whom the Software is
8+
furnished to do so, subject to the following conditions:
69

7-
1. Redistributions of source code must retain the above copyright notice, this
8-
list of conditions and the following disclaimer.
9-
2. Redistributions in binary form must reproduce the above copyright notice,
10-
this list of conditions and the following disclaimer in the documentation
11-
and/or other materials provided with the distribution.
10+
The above copyright notice and this permission notice shall be included in all
11+
copies or substantial portions of the Software.
1212

13-
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
14-
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
15-
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
16-
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
17-
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
18-
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
19-
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
20-
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
21-
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
22-
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
23-
24-
The views and conclusions contained in the software and documentation are those
25-
of the authors and should not be interpreted as representing official policies,
26-
either expressed or implied, of the FreeBSD Project.
13+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
14+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
15+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
16+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
17+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
18+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
19+
SOFTWARE.

‎MANIFEST.in

+4
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
1+
LICENSE
2+
README.md
3+
recursive-include docs *.md *.rst
4+
recursive-include examples *.md *.rst

‎README.md

+3-3
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@
22
[![Build Status](https://travis-ci.org/kundajelab/dragonn.svg?branch=master)](https://travis-ci.org/kundajelab/dragonn)
33
[![License](https://img.shields.io/github/license/mashape/apistatus.svg?maxAge=2592000)](https://github.com/cangermueller/deepcpg/tree/master/LICENSE)
44

5-
Python package for predicting single-cell CpG methylation states from DNA sequence and neighboring CpG sites using deep neural networks ([Angermueller et al., 2016](http://biorxiv.org/content/early/2017/02/01/055715)).
5+
Python package for predicting single-cell CpG methylation states from DNA sequence and neighboring CpG sites using deep neural networks ([Angermueller et al., 2017](http://biorxiv.org/content/early/2017/02/01/055715)).
66

77
```
8-
Angermueller, Christof, Heather Lee, Wolf Reik, and Oliver Stegle. “Accurate Prediction of Single-Cell DNA Methylation States Using Deep Learning.” bioRxiv, May 27, 2016, 055715. doi:10.1101/055715.
8+
Angermueller, Christof, Heather Lee, Wolf Reik, and Oliver Stegle. “Accurate Prediction of Single-Cell DNA Methylation States Using Deep Learning.” bioRxiv, February 1, 2017, 55715. doi:10.1101/055715.
99
```
1010

1111
<figure>
@@ -128,7 +128,7 @@ This command predicts missing methylation states of all cells and chromosomes an
128128

129129
## Examples <a name='examples'></a>
130130

131-
Interactive examples on how to use DeepCpG can be found [here](./examples/README.md).
131+
Interactive examples on how to use DeepCpG can be found [here](./examples/index.md).
132132

133133

134134

‎deepcpg/models/cpg.py

+6
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,9 @@
1+
"""CpG models.
2+
3+
Provides models trained observed neighboring methylation states of multiple
4+
cells.
5+
"""
6+
17
import inspect
28

39
from keras import layers as kl

‎deepcpg/models/dna.py

+5
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,8 @@
1+
"""DNA models.
2+
3+
Provides models trained with DNA sequence windows.
4+
"""
5+
16
import inspect
27

38
from keras import layers as kl

‎docs/source/basics.rst

-35
This file was deleted.

‎docs/source/index.rst

+35-13
Original file line numberDiff line numberDiff line change
@@ -1,25 +1,47 @@
1-
.. DeepCpG documentation master file, created by
2-
sphinx-quickstart on Sun Jan 29 21:26:20 2017.
3-
You can adapt this file completely to your liking, but it should at least
4-
contain the root `toctree` directive.
1+
DeepCpG: Deep neural networks for predicting single-cell DNA methylation
2+
========================================================================
3+
4+
Python package for predicting single-cell CpG methylation states from DNA sequence and neighboring CpG sites using deep neural networks.
5+
6+
Angermueller, Christof, Heather Lee, Wolf Reik, and Oliver Stegle. `Accurate Prediction of Single-Cell DNA Methylation States Using Deep Learning. <http://biorxiv.org/content/early/2017/02/01/055715>`_ bioRxiv, February 1, 2017, 55715. doi:10.1101/055715.
7+
8+
.. note::
9+
The documentation is still incomplete and will be extended soon.
10+
11+
12+
Installation
13+
------------
14+
15+
Clone the DeepCpG repository into your current directory:
16+
17+
.. code:: bash
18+
19+
git clone https://github.com/cangermueller/deepcpg.git
20+
21+
22+
Install DeepCpG and its dependencies:
23+
24+
.. code:: bash
25+
26+
python setup.py install
27+
528
629
Examples
7-
========
30+
--------
831

9-
.. toctree::
10-
:maxdepth: 2
32+
Interactive examples on how to use DeepCpG can be found `here <https://github.com/cangermueller/deepcpg/tree/master/examples>`_.
1133

12-
basics
1334

14-
API
15-
===
35+
API documentation
36+
-----------------
37+
.. toctree::
38+
:maxdepth: 2
1639

17-
.. automodule:: deepcpg.motifs
18-
:members:
40+
models/index
1941

2042

2143
Indices and tables
22-
==================
44+
------------------
2345

2446
* :ref:`genindex`
2547
* :ref:`modindex`

‎docs/source/models/index.rst

+25
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,25 @@
1+
.. _libdoc_model:
2+
3+
=====================================
4+
:mod:`model` -- model: DeepCpG models
5+
=====================================
6+
7+
The models package provides functionalities for building and training models.
8+
9+
Model utils
10+
===========
11+
12+
.. automodule:: deepcpg.models.utils
13+
:members:
14+
15+
CpG models
16+
==========
17+
18+
.. automodule:: deepcpg.models.cpg
19+
:members:
20+
21+
DNA models
22+
==========
23+
24+
.. automodule:: deepcpg.models.dna
25+
:members:

‎examples/README.md renamed to ‎examples/index.md

File renamed without changes.

‎setup.py

+7-2
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@ def read(fname):
1313
long_description=read('README.md'),
1414
author='Christof Angermueller',
1515
author_email='[email protected]',
16-
license="BSD",
16+
license="MIT",
1717
url='https://github.com/cangermueller/deepcpg',
1818
packages=find_packages(),
1919
install_requires=['h5py',
@@ -25,5 +25,10 @@ def read(fname):
2525
'pytest',
2626
'keras',
2727
'matplotlib',
28-
'seaborn']
28+
'seaborn'],
29+
keywords=['Deep learning',
30+
'Deep neural networks',
31+
'Epigenetics',
32+
'DNA methylation',
33+
'Single cells']
2934
)

0 commit comments

Comments
 (0)