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SCCAF-D Reproducibility

This repository contains Jupyter notebooks and codes to reproduce the results and figures published in the paper.

"Alleviating batch effects in cell type deconvolution".

Repository Structure

The repository is organized as follows:

Fig. 1: includes the codes of Main figure 1.

Fig. 3: includes the codes of Main figure 3.

Fig. 4: includes the codes of Main figure 4.

Fig. 5: includes the codes of Main figure 5.

Fig. 6: includes the codes of Main figure 6.

The dataset used in https://doi.org/10.6084/m9.figshare.27263982.v1.

Citation

For citation and further information please refer to this:

Feng, S., Huang, L., Pournara, A.V. et al. Alleviating batch effects in cell type deconvolution with SCCAF-D. Nat Commun 15, 10867 (2024). https://doi.org/10.1038/s41467-024-55213-x.

Thank you for your interest in our work.

Issues

If you encounter any issues or have questions about the code or analysis, please open an issue on the GitHub repository.

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example of applying SCCAF-D

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