https://github.com/pwwang/immunopipe-zhengy-2020

Reanalysis of the scRNA-seq and scTCR-seq data from Zheng, Y., et al. 2020 using immunopipe.
https://github.com/pwwang/immunopipe-zhengy-2020

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Reanalysis of the scRNA-seq and scTCR-seq data from Zheng, Y., et al. 2020 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-zhengy-2020
• Owner: pwwang
• Created: 2023-12-31T04:34:18.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T20:28:07.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:04.277Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 45 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# immunopipe-ZhengY-2020

Reanalysis of the scRNA-seq and scTCR-seq data from [Zheng, Y., et al. 2020](https://www.nature.com/articles/s41467-020-20019-0) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Zheng, Y., Chen, Z., Han, Y., Han, L., Zou, X., Zhou, B., Hu, R., Hao, J., Bai, S., Xiao, H., Li, W. V., Bueker, A., Ma, Y., Xie, G., Yang, J., Chen, S., Li, H., Cao, J., & Shen, L. (2020). Immune suppressive landscape in the human esophageal squamous cell carcinoma microenvironment. Nature Communications, 11(1), 1-17.](https://www.nature.com/articles/s41467-020-20019-0)

## Data preparation

The data was downloaded from [GSE145370](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145370), where 14 samples from 7 patients were sequenced with scRNA-seq and scTCR-seq.

See `prepare-data.sh` for details.

## Configuration

> [!NOTE]

> This is not a replication of the original paper, primarily due to the irreproducibility of the clustering results. This is a reanalysis of the data using [`immunopipe`](https://github.com/pwwang/immunopipe), showing the potential of the pipeline similar analyses listed in the paper.

>

The configuration in `SeuratClusterStats` section was setup based on Fig 2. The clononality analysis was performed by `Immunarch` by default.

See details at `Immunopipe.config.toml`.

## Results/Reports

You can find the results in the `Immunopipe-output` directory.

The report can be found at [https://imp-zhengy-2020.pwwang.com/REPORTS](https://imp-zhengy-2020.pwwang.com/REPORTS).