Getting Started =============== Installation ------------ Geneformer installation instructions. Make sure you have git-lfs installed (https://git-lfs.com). .. code-block:: bash git lfs install git clone https://huggingface.co/ctheodoris/Geneformer cd Geneformer pip install . Tutorials --------- | See `examples `_ for: | - tokenizing transcriptomes | - pretraining | - hyperparameter tuning | - fine-tuning | - extracting and plotting cell embeddings | - in silico perturbation Please note that the fine-tuning examples are meant to be generally applicable and the input datasets and labels will vary dependent on the downstream task. Example input files for a few of the downstream tasks demonstrated in the manuscript are located within the `example_input_files directory `_ in the dataset repository, but these only represent a few example fine-tuning applications. Tips ---- Please note that GPU resources are required for efficient usage of Geneformer. Additionally, we strongly recommend tuning hyperparameters for each downstream fine-tuning application as this can significantly boost predictive potential in the downstream task (e.g. max learning rate, learning schedule, number of layers to freeze, etc.).