HCC-IMC processing pipeline

Table of Contents

1. About The Project
2. System requirement
   • Operating systems
   • Software dependencies
3. Usage
4. Roadmap
5. Contributing
6. License
7. Contact
8. Acknowledgements

About The Project

This project proposed a computational pipeline to analyze the tumor microenvironment in treatment-naive pancreatic adenocarcinoma patients. The cohort was previously described in our Cancer Discovery paper

System requirement

Operating systems

The computational pipeline was developed on the following operating system:

• Dell Precision 5820 computer with Windows 10 Pro for Workstations operating systems version.
• Processor: Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz 3.91GHz
• 32GB RAM
• 64-bit operating system, x64-based processor.

Software dependencies

The computational pipeline was developed using the following softwares:

• R version 3.5.3.
• Rstudio Desktop version 1.4.
• Python version 3.8
• Pycharm Python IDE version 2020.3.3.
• R packages listed at the beginning of each R script.
• BioRender

Installation guide

Instructions

To install the pipeline, simply download the codes and run from local R or Python compiler.

Installation time

• Installation time all dependencies should take no longer than 30 minutes.
• Codes can be readily used upon downloading and do not require extra installations.

Usage

The pipeline consists of five components:

• PDAC_IHCpipeline0.R (Data preprocessing, patient group split, first-order characterization)
• PDAC_IHCpipeline1.R (mIRS computation)
• PDAC_IHCpipeline2.R (immune aggregations computation)
• PDAC_IHCpipeline_validation.R (validation of biomarkers on a neoadjuvant-treated cohort)
• Function.R (Custom R functions defined for computations)

License

Distributed under the MIT License. See LICENSE for more information.

Contact

Haoyang Mi - hmi1@jhmi.edu