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

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.

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
additional		additional
datasets_prepro		datasets_prepro
scPI		scPI
Cortex-clustering.ipynb		Cortex-clustering.ipynb
Cortex-imputation.ipynb		Cortex-imputation.ipynb
Cortex-loglikelihood-test.ipynb		Cortex-loglikelihood-test.ipynb
README.md		README.md
demo_scPI-FA_cortex.ipynb		demo_scPI-FA_cortex.ipynb
demo_scPI-ZIFA-cortex.ipynb		demo_scPI-ZIFA-cortex.ipynb
demo_scPI-ZINB_cortex.ipynb		demo_scPI-ZINB_cortex.ipynb
demo_scVI_cortex.ipynb		demo_scVI_cortex.ipynb
repeat_FA_cortex.py		repeat_FA_cortex.py
repeat_ZIFA_cortex.py		repeat_ZIFA_cortex.py
repeat_ZINB_cortex.py		repeat_ZINB_cortex.py
utils.py		utils.py