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

Reanalysis of the scRNA-seq and scTCR-seq data from Eberhardt, Christiane S., et al., 2021 using immunopipe.
https://github.com/pwwang/immunopipe-eberhardtcs-2021

Last synced: 14 days ago
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Reanalysis of the scRNA-seq and scTCR-seq data from Eberhardt, Christiane S., et al., 2021 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-eberhardtcs-2021
• Owner: pwwang
• Created: 2023-12-31T06:45:08.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T05:59:04.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:03.976Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 16.1 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# immunopipe-EberhardtCS-2021

Reanalysis of the scRNA-seq and scTCR-seq data from [Eberhardt, Christiane S., et al., 2021](https://www.nature.com/articles/s41586-021-03862-z) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Eberhardt, Christiane S., et al. "Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer." Nature 597.7875 (2021): 279-284.](https://www.nature.com/articles/s41586-021-03862-z)

>

## Data preparation

The data was downloaded from [GSE180268](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180268), where 6 samples from 6 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.

>

We used a minimal configuration for the analysis, which includes very basic steps such as cell filtering, clustering, and differential expression analysis. 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-eberhardtcs-2021.pwwang.com/REPORTS](https://imp-eberhardtcs-2021.pwwang.com/REPORTS).