https://github.com/pwwang/immunopipe

Integrative analysis for scTCR- and scRNA-seq data
https://github.com/pwwang/immunopipe

Last synced: 14 days ago
JSON representation

Integrative analysis for scTCR- and scRNA-seq data

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe
• Owner: pwwang
• License: gpl-3.0
• Created: 2021-05-18T22:08:18.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2024-12-10T20:38:19.000Z (23 days ago)
• Last Synced: 2024-12-10T21:29:07.473Z (23 days ago)
• Language: Python
• Homepage: https://pwwang.github.io/immunopipe
• Size: 23.8 MB
• Stars: 13
• Watchers: 4
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


  



Integrative analysis for single-cell RNA sequencing and single-cell TCR sequencing data



`immunopipe` is a pipeline based on [`pipen`](https://github.com/pwwang/pipen) framework. It includes a set of processes for scTCR- and scRNA-seq data analysis in `R`, `python` and `bash`. The pipeline is designed to be flexible and configurable.



  



See a more detailed flowchart [here](https://github.com/pwwang/immunopipe/blob/dev/docs/immunopipe.flowchart.png?raw=true).

## Documentaion

[https://pwwang.github.io/immunopipe](https://pwwang.github.io/immunopipe)

## Proposing more analyses

If you have any suggestions for more analyses, please feel free to open an issue [here](https://github.com/pwwang/immunopipe/issues/new)

## Example

[https://github.com/pwwang/immunopipe-example](https://github.com/pwwang/immunopipe-example)

## Gallery

There are some datasets with both scRNA-seq and scTCR-seq data available in the publications. The data were reanalyzed using `immunopipe` with the configurations provided in each repository, where the results are also available.

Check out the [gallery](https://pwwang.github.io/immunopipe/gallery) for more details.