Method for simulating single cells using longitudinal scRNA-seq.
Project description
prescient
Software for PRESCIENT (Potential eneRgy undErlying Single Cell gradIENTs), a generative model for modeling single-cell time-series.
- Documentation available at prescient.github.io.
- 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.
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)
Documentation
Documentation is available at https://cgs.csail.mit.edu/prescient.
Bugs & Suggestions
Please report any bugs, problems, suggestions or requests as a Github issue
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
prescient-0.0.2.tar.gz
(13.2 kB
view hashes)
Built Distribution
prescient-0.0.2-py3-none-any.whl
(17.3 kB
view hashes)
Close
Hashes for prescient-0.0.2-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | dfc9ad05ab7b0a77f45b6fb14527795c2d648313d1718e51c42f96d1fbd7aee8 |
|
MD5 | 24822ef08051b15356d8447507b4d82b |
|
BLAKE2b-256 | 9bb2edbc6a0af0faf25fdf0d645f76987b65dc44777cb9abc072eb474ebf4562 |