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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.