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germline-epitopes's Introduction

Germline epitope burden (GEB)

Code repository of publication: Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity (Houlahan et al., 2023)

📁 Repository content

This GitHub repository contains the following folders:

└─ data/: directory containing source data to reproduce figures
└─ figures/: directory containing R and other code to reproduce figures
└─ supplementary_figures/: directory containing R and other code to reproduce supplementary figures
└─ supplementary_tables/: directory containing R and other code to reproduce supplementary tables

◼️ Prerequisites

BoutrosLab.plotting.general (v6.0.1)
ConsensusClusterPlus (v1.50.0)
GenomicRanges (v1.38.0)
survminer (v0.4.8)
metafor (2.4-0)
caret (v6.0-86)
tidyr (v1.1.4)
pec (v2019.11.03)

✅ Citation

Kathleen E. Houlahan, Aziz Khan, Noah F Greenwald, Robert B. West, Michael Angelo, Christina Curtis. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity, bioRxiv (2023); doi: https://doi.org/10.1101/2023.03.15.532870

✉️ Contact

For any questions, please contact Kathleen Houlahan [email protected]

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