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https://github.com/bostongene/pdac.tme.george

https://github.com/bostongene/pdac.tme.george

Science Score: 26.0%

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Repository

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  • Host: GitHub
  • Owner: BostonGene
  • License: other
  • Language: HTML
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  • Size: 27.5 MB
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Created over 2 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

N|Solid

PDAC Tumor Microenvironment Classification

This repository contains the code and resources for classifying the tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) based on functional gene signatures (FGEs) calculated on bulk RNA-Seq or microarray gene expressions data.

Overview

PDAC presents a complex tumor environment, which has historically posed challenges in the development of reliable predictive biomarkers for targeted therapies and immunomodulation. To address this, we've implemented a classification approach based on transcriptomic profiling of the TME.

Four TME subtypes were developed: * Immune Enriched (IE) * Immune Enriched, Fibrotic (IE/F) * Fibrotic (F) * Immune Depleted (D)

Publication

Developed classification is described in details in the manuscript.

plot

Features

This repository contains: + Data * PDAC Meta-Cohort: annotation & calculated FGEs for all samples * ICGC PACA-CA (test cohort): annotation & expressions + Genesets * genesets/PAAD_genesets.gmt - table of all used genesets + Code * utils/ - scripts for data preprocessing, ssGSEA score calculation, median scaling and plots * Notebook MFPTMEclassificataion.ipynb with a classification of ICGC PACA-CA samples into four TME subtypes using supervised clustering

Getting Started

Prerequisites

  • Python 3.x - Python 3.9 is advised
  • Required Python libraries: please see requirements.txt ### Installation Clone the repository: git clone https://github.com/BostonGene/PDAC.TME.George.git Navigate to the repository directory: cd PDAC.TME.George Install required dependencies:
    python3.9 -m venv venv source venv/bin/activate venv/bin/python3.9 -m pip install --upgrade pip pip install --no-deps -r requirements.txt jupyter nbextension enable --py widgetsnbextension python -m ipykernel install --user --name=pdac_tme_venv

License

Licensed by BostonGene Licence -- for more info please see LICENSE file
Please direct any inquiries concerning usage to askusepermission@bostongene.com.
© 2023 BostonGene Corporation.

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