Adventitial_scRNAseq

Code and results from the paper "Single-Cell RNA-Seq Reveals Adventitial Fibroblast Alterations during Mouse Atherosclerosis"

Setup

Conda environment used for all analyses is available via the environment.yaml file

This includes all packages and versions used for analysis

R packages are included in the r_packages.txt file and can be loaded with the following lines in R after the conda environment is built:

# Load package list
packages <- readLines("r_packages.txt")

# Install missing packages
for (pkg in packages) {
  if (!require(pkg, character.only = TRUE)) {
    install.packages(pkg, repos = "https://cloud.r-project.org/")
     }
}

Scripts

All code used to analyze the data and produce graphs and results can be found in the JupyterNotebooks folder

• The notebooks for analysis of all cells start with 'step#'
• The notebooks for analysis of fibroblast subsets start with 'subsetFibroblasts'
• The notebooks for analysis of the human plaque vs proximal samples start with 'human'

For each section all notebooks were run in their step order

Data availability

All original data is available at GEO accession number GSExxxxxx