immunopipe 2.4.0

A pipeline for integrative analysis for scRNA-seq and scTCR-/scBCR-seq data

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

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immunopipe is a pipeline based on 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.

See a more detailed flowchart here.

Documentaion

https://pwwang.github.io/immunopipe

Proposing more analyses

If you have any suggestions for more analyses, please feel free to open an issue here

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 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.