Metadata-Version: 2.4
Name: immunopipe
Version: 2.1.0
Summary: A pipeline for integrative analysis for scRNA-seq and scTCR-/scBCR-seq data
License: GNU General Public License v3.0
License-File: LICENSE
Author: pwwang
Author-email: pwwang@pwwang.com
Requires-Python: >=3.9,<4.0
Classifier: License :: Other/Proprietary License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Provides-Extra: cli-gbatch
Provides-Extra: diagram
Provides-Extra: runinfo
Requires-Dist: biopipen (>=0.34.16,<0.35.0)
Requires-Dist: pipen-cli-gbatch (>=0.1,<0.2) ; extra == "cli-gbatch"
Requires-Dist: pipen-diagram (>=0.13,<0.14) ; extra == "diagram"
Requires-Dist: pipen-runinfo (>=0.9,<0.10) ; extra == "runinfo"
Project-URL: Homepage, https://github.com/pwwang/immunopipe
Project-URL: Repository, https://github.com/pwwang/immunopipe
Description-Content-Type: text/markdown

<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/BCR sequencing data</p>
<hr />

`immunopipe` is a pipeline based on [`pipen`](https://github.com/pwwang/pipen) framework. It includes a set of processes for scRNA-seq and scTCR-/scBCR-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-/scBCR-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.

## Citation

If you use `immunopipe` in your research, please cite the following paper:

- [Wang, P., Yu, Y., Dong, H., Zhang, S., Sun, Z., Zeng, H., ... & Li, Y. (2025). Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline. NAR Genomics and Bioinformatics, 7(2), lqaf063.](https://academic.oup.com/nargab/article/7/2/lqaf063/8136476)

