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

Reanalysis of the scRNA-seq and scTCR-seq data from Gate, David, et al., 2021 using immunopipe.
https://github.com/pwwang/immunopipe-gated-2021

Last synced: 14 days ago
JSON representation

Reanalysis of the scRNA-seq and scTCR-seq data from Gate, David, et al., 2021 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-gated-2021
• Owner: pwwang
• Created: 2023-12-31T06:11:07.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T18:54:24.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:00.781Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 9.37 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# immunopipe-GateD-2021

Reanalysis of the scRNA-seq and scTCR-seq data from [Gate, David, et al., 2021](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122025/) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Gate, David, et al. "CD4+ T cells contribute to neurodegeneration in Lewy body dementia." Science 374.6569 (2021): 868-874.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122025/)

>

## Data preparation

The data was downloaded from [GSE161192](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161192), where 4 samples from 2 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`.

The paper also focused on all of the cells, rathen than T cells. To do that, on could propose a configuration file without T cell selection, and remove `TCRData` from the input file.

## Results/Reports

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

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