scRNA-seq and Xenium spatial transcriptomic analysis of human carotid artery plaque samples

• List of python packages and Python version can be found in environment.yaml file
• At the beginning of each .Rmd file, the folder where R packages were installed is set. Change this path accordingly to your R-packge folder.
• Folder structure:
  • scRNA-seq alignment should be done on an HPC cluster. Change the the paths of raw_data_path and output_path in run_cellranger_count.sh to your path if wish to run the alignment.
  • Set up a base_dir, which contains:
    • The raw Xenium data in a folder called xenium_data
    • The root folder of the code (preferentially named src)
    • The folder aligned_data, which contains the output of the scRNA-seq alignment script, i.e. the aligned data

1. scRNA-seq

   1. Alignment

      • Code for the alignment is in the alignment_code folder.
      • First create a referemce genome with run_cellranger_mkref.sh. If you wish, change the parameters of reference genome creation within the code.
      • Then run run_cellranger_count.sh. If you wish, change the parameters of alignment within the code.

   2. Analysis of aligned data

      • Code of the scRNA-seq analysis is contained in scrna_analysis folder
      • Analysis of cell counts: notebooks starting with "ath" should be executed in the order of number indicated in the prefix of their names
      • The two Notebooks analysing the dataset of GSE159677 dataset have to be executed before starting ath_8_1... .ipnyb Notebook
      • Information about the analysis steps can be found in the individual notebook

2. Xenium spatial transcriptomics

   1. Custom cell segmentation

      • Code is in the cell_segmentation folder with own Readme.me file
      • Detailed Readme file contains information about cell segmentation steps

   2. Processed spatial transcriptomic analysis

      • Code of spatiel transciptomic analysis can be found in xenium_analysis folder
      • Notebooks starting with "xen" should be executed in the order of number indicated in the prefix of their names
      • Information about the analysis steps can be found in the individual notebook