THOR code and additional files

Publications

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.