perturbvi is a scalable approach to infer regulatory modules through informative latent component model in the single-cell Perturb-seq data.
Installation | Example | Notes | Version | Support | Other Software
Users can download the latest repository and then use pip:
git clone https://github.com/mancusolab/perturbvi.git
cd perturbvi
pip install .TBD
perturbviuses JAX with Just In Time compilation to achieve high-speed computation. However, there are some issues for JAX with Mac M1 chip. To solve this, users need to initiate conda using miniforge, and then installperturbviusingpipin the desired environment.
TBD
Please report any bugs or feature requests in the Issue Tracker. If users have any questions or comments, please contact Dong Yuan ([email protected]) and Nicholas Mancuso ([email protected]).
Feel free to use other software developed by Mancuso Lab:
- SuShiE: a Bayesian fine-mapping framework for molecular QTL data across multiple ancestries.
- MA-FOCUS: a Bayesian fine-mapping framework using TWAS statistics across multiple ancestries to identify the causal genes for complex traits.
- SuSiE-PCA: a scalable Bayesian variable selection technique for sparse principal component analysis
- twas_sim: a Python software to simulate TWAS statistics.
- FactorGo: a scalable variational factor analysis model that learns pleiotropic factors from GWAS summary statistics.
- HAMSTA: a Python software to estimate heritability explained by local ancestry data from admixture mapping summary statistics.
perturbvi is distributed under the terms of the
MIT license.
This project has been set up using Hatch. For details and usage information on Hatch see https://github.com/pypa/hatch.