Probabilistic models of scRNA-seq
Package to reproduce results in my MSc Thesis. It implements wrappers (to standardize model calling) and utility methods (to output results) which facilitate model comparison in a set of benchmarking tasks.
See the pre-print for details.
Requirements
Install via python setup.py install.
Need to install mpCMF and ZINBayes.
R needs to be installed with ZINB-WaVE and pCMF packages.
See data/README.md for information about data sets.
Acknowledgements
The code to perform imputation tests and to run ZIFA, ZINB-WaVE and scVI was partly adapted from scVI-reproducibility. ZIFA was originally implemented here.