<p align="center">
<img height="120" style="height: 120px" src="https://github.com/pwwang/immunopipe/blob/dev/docs/logo.png?raw=true" />
</p>
<p align="center">Integrative analysis for single-cell RNA sequencing and single-cell TCR sequencing data</p>
<hr />
`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.
<p align="center">
<img src="https://github.com/pwwang/immunopipe/blob/dev/docs/immunopipe.ms.png?raw=true" />
</p>
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.
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