https://github.com/pwwang/immunopipe-elhama-2018

Reanalysis of the scRNA-seq and scTCR-seq data from Azizi, Elham, et al. 2018 using immunopipe.
https://github.com/pwwang/immunopipe-elhama-2018

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Reanalysis of the scRNA-seq and scTCR-seq data from Azizi, Elham, et al. 2018 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-elhama-2018
• Owner: pwwang
• Created: 2023-12-28T23:48:52.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-27T16:42:22.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:03.386Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 27.7 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# immunopipe-ElhamA-2018

Reanalysis of the scRNA-seq and scTCR-seq data from [Azizi, Elham, et al. 2018](https://www.cell.com/cell/fulltext/S0092-8674(18)30723-2) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Azizi, Elham, et al. "Single-cell map of diverse immune phenotypes in the breast tumor microenvironment." Cell 174.5 (2018): 1293-1308.](https://www.cell.com/cell/fulltext/S0092-8674(18)30723-2)

## Data preparation

The data was downloaded from [GSE114724](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114724), where 5 samples from 3 patients (BC9, BC10 and BC11) 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`](https://github.com/pwwang/immunopipe), showing the potential of the pipeline similar analyses listed in the paper.

>

The original paper used diffusion map components that are associated with Activation, Hypoxia and Terminal Differentiation to study the T-cell characteristics. The reduction was done on 8 samples (BC1-8), which were not provided in the GEO dataset. We are not able to replicate the exact scores for the diffusion map components. However, `immunopipe` can still calculate the diffusion map components for the samples in the dataset, with the only 3 patients in this dataset. The diffusion map components may not be comparable to the original paper, but used to show the potential of `immunopipe` in similar analyses.

## Results/Reports

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

The report can be found at [https://imp-elhama-2018.pwwang.com/REPORTS](https://imp-elhama-2018.pwwang.com/REPORTS).