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

"Brain Cell Atlas: An Integrative Ensemble of Cell Transcriptomes Across Human Brain Regions"

The web portal of Brain Cell Atlas together with all the datasets are publicly available at www.braincellatlas.org and mirror.braincellatlas.org.

The repository is organized as follows:

• notebooks: This folder contains Jupyter notebooks that cover all the code related to generating the main figures and the extended data figures of the Brain Cell Atlas project. Each notebook focuses on one figure, making it easy to navigate and reproduce specific results.

• data: This folder contains some input data for running the code in the notebooks. Due to the store limitation, some of the large data files are not included in the repository. However, instructions are provided on how to obtain the required data.

• results: This folder stores the output files generated by the notebooks.

• figures: This folder stores the output figures generated by the notebooks.

• scripts: this folder contains codes for supplementary figures, supporting scripts and utilities used in the analysis pipelines. These scripts provide additional functionality and can be used independently or in combination with the notebooks.

Please note that some of the large files in the data and results folders, which are necessary for running the code, are not included in this repository due to their large size. They were uploaded to Zenodo (https://zenodo.org/uploads/11195725).

For label transfer to the Brain Cell Atlas, the documentation of scAnnot is available at https://github.com/rnacentre/scAnnot.

For citation and further information please refer to the Research Square preprint:

Chen, X. et al. Brain Cell Atlas: An integrative ensemble of cell transcriptomes across human brain regions. Research Square (2023) doi:10.21203/rs.3.rs-3221500/v1.

Thank you for your interest in our work. We hope you find the code and resources provided here useful in reproducing and building upon the findings of the Brain Cell Atlas project.

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