Final Project

Skeleton for neural network project.

assignment

1. Implement an 8x3x8 autoencoder.
2. Implement a neural network to identify RAP1 transcription factor binding sites. #. Apply the RAP1 network to test data to predict binding sites.

structure

Autoencoder contained in neuralnet.py. RAP1 neural network contained in rap1net.py. Output sequences and scores from test data are contained in TestOutput.txt.

usage

To use the package, first run

conda install --yes --file requirements.txt

to install all the dependencies in requirements.txt. Then the package's main function (located in hw2skeleton/__main__.py) can be run as follows

python -m hw2skeleton -P data test.txt

testing

Testing is as simple as running

python -m pytest

from the root directory of this project.

contributors

Original design by Scott Pegg. Refactored and updated by Tamas Nagy.