Scanning the transcriptome for ago2:miRNA to mRNA binding sites and predicting fold change

Running example models and evaluation

Set up the environment

Create a conda env by running conda create --name YOUR_ENVIRONMENT_NAME --file spec-file.txt

Activate an existing environment by conda activate YOUR_ENVIRONMENT_NAME

Download the data

Run ./data/download_data_for_ML.sh which installs the gdown package (if not installed yet) through pip and downloads the datasets.

Installing the gdown through pip is temporary until we fix installing through conda

Example ML notebooks

After you download the datasets, you can play with example notebooks ML_training_and_evaluation.regression.ipynb and ML_training_and_evaluation.classification.ipynb. Choose the environment YOUR_ENVIRONMENT_NAME you created before as your notebook kernel.