/COVID_IFN_omics

Omics profile of COVID patients based on interferon

Primary LanguageShellApache License 2.0Apache-2.0

Systemic multiomics analysis defines the heterogenous interferon response landscape in COVID-19 severity

Description

Multi-omics characterization of COVID-19 patients based on interferon profile

Installation

Clone the repository

git clone https://github.com/neogilab/COVID_IFN_omics.git
cd COVID_IFN_omics

Requirements

  1. A linux distribution

  2. R and R studio environment and following packages Open R and run

# install and load  the package  manager
 if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
    
 bio_pkgs <- c("ComplexHeatmap", "ggpubr", "ggplot2", "ggvenn", 
          "Hmisc", "GSVA", "limma", "DESeq2", "ConsensusClusterplus")

# install:
BiocManager::install(bio_pkgs)

Run code

  1. Create folders
Rscript create_folders.R
  1. Move data files to folder data
  2. Change path to your own computer
  3. Execute R notebooks for producing tables and figures

Author

Flora Mikaeloff