This repository contains the code and supplementary files for the publication of results from Project THOR (Targeting Smooth Muscle Cells in Atherosclerosis Therapy), which is part of the Open Discovery Innovation Network (ODIN) initiative. See also: https://doi.org/10.5281/zenodo.7327363 Publications Preprint: Mapping atherogenesis mechanisms in smooth muscle cells by targeting genes linked to coronary artery disease Julián Albarrán-Juárez et al. bioRxiv 2024.11.11.623011; doi: https://doi.org/10.1101/2024.11.11.623011 Files description 1-1_athero-scrnaseq-integration.Rmd - R Markdown file containing the integration of publicly available single-cell RNA sequencing data on human atherosclerosis (2021-2024). 1-2_athero-scrnaseq-integration.Rmd - HTML report on the integration and analysis of scRNA-seq dataset. 1-3_athero-scrnaseq-annotation.ipynb - Cell type annotation of scRNA-seq dataset using popV algorithm. 2-1_bulk-rnaseq-preprocessing.md - Markdown file describing preprocessing steps of bulk RNA-seq data on HPC (from FASTQ files to count matrices). 2-2_bulk-rnaseq-analysis.R - R script file containing the code for bulk RNA-seq data analysis and integration. 2-3_bulk-rnaseq-regulon-enrichment.R - R script file containing the code for TF motif enrichment analysis. 2-4_bulk-rnaseq-gcn-analysis.R - R script file containing the code for building and exploring a gene co-expression network based on control samples in bulk RNA-seq data. 2-5_bulk-rnaseq-celltype-deconvolution.R - R script file containing the code for cell type deconvolution of bulk RNA-seq samples using the integrated scRNA-seq dataset as reference. deg_functions.R - R script file containing helper functions for bulk RNA-seq data analysis. nfcore-rnaseq-qc-reports.zip - Archive with HTML reports for quality control after bulk RNA-seq preprocessing with 'nf-core/rnaseq' pipeline. scrnaseq_sample_info.tsv - information about publicly available scRNA-seq data on human atherosclerosis (2021-2024). THOR_Knockdown_Genes_R1-2.tsv - text file containing information about THOR target genes.