prescient

Software for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs), a generative model for modeling single-cell time-series.

• Current paper version: https://www.biorxiv.org/content/10.1101/2020.08.26.269332v1
• For paper pre-processing scripts, training bash scripts, pre-trained models, and visualization notebooks please visit https://github.com/gifford-lab/prescient-analysis.

Documentation

Documentation is available at https://cgs.csail.mit.edu/prescient.

Requirements

• pytorch 1.4.0
• geomloss 0.2.3, pykeops 1.3
• numpy, scipy, pandas, sklearn, tqdm, annoy
• scanpy, pyreadr, anndata
• Recommended: An Nvidia GPU with CUDA support for GPU acceleration (see paper for more details on computational resources)

Bugs & Suggestions

Please report any bugs, problems, suggestions or requests as a Github issue