pwwang / immunopipe-ZhengY-2020

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

immunopipe-ZhengY-2020

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

Data preparation

The data was downloaded from 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, 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.