https://github.com/pwwang/immunopipe-cheonis-2021

Reanalysis of the scRNA-seq and scTCR-seq data from Cheon, I. S., 2021 using immunopipe.
https://github.com/pwwang/immunopipe-cheonis-2021

Last synced: 14 days ago
JSON representation

Reanalysis of the scRNA-seq and scTCR-seq data from Cheon, I. S., 2021 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-cheonis-2021
• Owner: pwwang
• Created: 2023-12-31T05:02:22.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T05:28:23.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:01.996Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 11.9 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# immunopipe-CheonIS-2021

Reanalysis of the scRNA-seq and scTCR-seq data from [Cheon, I. S., 2021](https://www.science.org/doi/full/10.1126/sciimmunol.abk1741) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Cheon, I. S., Li, C., Son, Y. M., Goplen, N. P., Wu, Y., Cassmann, T., Wang, Z., Wei, X., Tang, J., Li, Y., Marlow, H., Hughes, S., Hammel, L., Cox, T. M., Goddery, E., Ayasoufi, K., Weiskopf, D., Boonyaratanakornkit, J., Dong, H., . . . Sun, J. (2021). Immune signatures underlying post-acute COVID-19 lung sequelae. Science Immunology.](https://www.science.org/doi/full/10.1126/sciimmunol.abk1741)

>

## Data preparation

The data was downloaded from [GSE176201](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176201), where 6 samples from 5 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.

>

The configuration is a minimal one, which includes very basic steps such as clustering, and differential expression analysis, together with a dotplot of signature genes shown in Figure 4 of the original paper. The configuration can be found in `Immunopipe.config.toml`.

## Results/Reports

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

The report can be found at [https://imp-cheonis-2021.pwwang.com/REPORTS](https://imp-cheonis-2021.pwwang.com/REPORTS).