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

Reanalysis of the scRNA-seq and scTCR-seq data from Mahuron, Kelly M., et al. 2020 using immunopipe.
https://github.com/pwwang/immunopipe-mahuronkm-2020

Last synced: 14 days ago
JSON representation

Reanalysis of the scRNA-seq and scTCR-seq data from Mahuron, Kelly M., et al. 2020 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-mahuronkm-2020
• Owner: pwwang
• Created: 2023-12-30T07:58:39.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T19:13:26.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:01.118Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 8.38 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# immunopipe-MahuronKM-2020

Reanalysis of the scRNA-seq and scTCR-seq data from [Mahuron, Kelly M., et al. 2020](https://rupress.org/jem/article/217/9/e20192080/151858/Layilin-augments-integrin-activation-to-promote) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Mahuron, Kelly M., et al. "Layilin augments integrin activation to promote antitumor immunity." Journal of Experimental Medicine 217.9 (2020).](https://rupress.org/jem/article/217/9/e20192080/151858/Layilin-augments-integrin-activation-to-promote)

>

## Data preparation

The data was downloaded from [GSE148190](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148190), where 2 samples from 1 patient 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 only selected 2 samples with paired scRNA-seq and scTCR-seq data available.

>

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`.

This demonstrates the potential of `immunopipe` for analyzing datasets with very few samples.

## Results/Reports

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

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