scDenorm_reproducibility

Overview

This repository contains Jupyter notebooks to reproduce the analyses presented in the manuscript "scDenorm: a denormalisation tool for Integrating Single-cell Transcriptomics Data."

Tutorial of running notebooks

• 1.download notebooks
• 2.download docker and data
• 3.move data to scDenorm_reproducibility/data folder
• 4.run docker image

Notebooks

The repository includes the following notebooks:

• Fig1.ipynb: Analysis for Figure 1
• Fig2.ipynb: Analysis for Figure 2
• Fig3.ipynb: Analysis for Figure 3
• Fig4.ipynb: Analysis for Figure 4
• Fig5.ipynb: Analysis for Figure 5
• Fig6.ipynb: Analysis for Figure 6
• Fig7.ipynb: Analysis for Figure 7

Environment configurations

• Python=3.2: config/environment.yaml
• R=4.0.2: config/installed_packages.csv

How to use and install scDenorm

• Install: pip install scDenorm
• Usage: scdenorm data/pbmc3k_norm.h5ad --fout data/pbmc3k_denorm.h5ad
• Documentation: https://changebio.github.io/scDenorm

Citation

Yin Huang, Anna Vathrakokili Pournara, Ying Ao, Hui Zhang, Yongjian Zhang, Sheng Liu, Alvis Brazma, Irene Papatheodorou, Xinlu Yang, Ming Shi, Zhichao Miao “scDenorm: a denormalisation tool for integrating single-cell transcriptomics data”(Under review)

For any questions or issues, please open an issue in the repository.