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# Decoding:
# Neural_Decoding:

### A python package that includes many methods for decoding neural activity

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This package accompanies a manuscript (soon to be released) that compares the performance of these methods on several datasets.


## Dependencies
In order to run all the decoders based on neural networks, you need to install [Keras] (https://keras.io/#installation) <br>
In order to run the XGBoost Decoder, you need to install [XGBoost] (https://pypi.python.org/pypi/xgboost/) <br>
In order to run the Wiener Filter or Wiener Cascade, you will need [scikit-learn] (http://scikit-learn.org/stable/install.html).


## Getting started
We have included jupyter notebooks that provide detailed examples of how to use the decoders. The file "Examples_kf_decoder" is for the Kalman filter decoder and the file "Examples_all_decoders" is for all other decoders.

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- **bin_spikes**: converts spike times to the number of spikes within time bins
- **bin_output**: converts a continuous stream of outputs to the average output within time bins
- **get_spikes_with_history**: using binned spikes as input, this function creates a covariate matrix of neural data that incorporates spike history

## Dependencies
In order to run all the decoders based on neural networks, you need to install [Keras] (https://keras.io/#installation) <br>
In order to run the XGBoost Decoder, you need to install [XGBoost] (https://pypi.python.org/pypi/xgboost/) <br>
In order to run the Wiener Filter or Wiener Cascade, you will need [scikit-learn] (http://scikit-learn.org/stable/install.html).

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