Installation

LncRNA-Py can be installed via GitHub and conda. Alternatively, one can use our Google Colab example notebooks [1, 2] as starting points.

git clone https://github.com/luukromeijn/lncRNA-Py.git

Required Dependencies

The required conda environment can be installed using the provided environment.yml file.

conda env create -f environment.yml

Alternatively, one can install the required packages manually. We find that the following order of installation will lead to the least tedious and cumbersome virtual environment setup.

conda create -n lncrna -y
conda activate lncrna

PyTorch for CPU only:

conda install pytorch torchvision torchaudio cpuonly -c pytorch -y

PyTorch for GPU:

conda install pytorch torchvision torchaudio pytorch-cuda=11.8 -c pytorch -c nvidia -y

We refer to the PyTorch website for the most up-to-date installation procedure.

Others:

conda install pytables -c conda-forge -y
conda install numpy pandas scikit-learn -c conda-forge -y
conda install matplotlib biopython huggingface_hub -c conda-forge -y
conda install anaconda::safetensors
conda install hugging
pip install umap-learn sentencepiece

Optional Dependencies

Some features require the installation of the following dependencies:

pip install viennarna
conda install tqdm xgboost pytest -c conda-forge -y
conda install bioconda::blast