YangLabHKUST / scPI

scPI: A scalable framework for probabilistic inference insingle-cell RNA-sequencing data analysis

scPI

scPI: A scalable framework for probabilistic inference insingle-cell RNA-sequencing data analysis

• Demonstration code of scPI.
• Reproducing the plots of the paper "scPI: A scalable framework for probabilistic inference insingle-cell RNA-sequencing data analysis".

System requirements

• Python 3.7.6 (version tested)
• Pytorch 1.4.0 (version tested)

Demo

• Follow the notebooks in "datasets_prepro" to prepare data.
• Follow the given demos. Here we provide demos for cortex dataset. If you want to apply scPI to analyze PBMC dataset, you only need to change "data_path" to match the path where you save the PBMC dataset.
• Output should match the paper.