Ekin-Kahraman/bulk-rnaseq-differential-expression: v1.0.0 - Bulk RNA-seq differential expression pipeline

Archival release of a reproducible bulk RNA-seq differential expression workflow for nasopharyngeal SARS-CoV-2 host-response analysis using GEO GSE152075. Scope This repository starts from the published count matrix and sample metadata provided through GEO. It does not perform raw-read processing, alignment, or quantification. The focus is downstream differential expression, enrichment analysis, reproducibility, and result validation. Contents Quality control and balanced subset construction PCA and exploratory visualization DESeq2 differential expression analysis apeglm log2 fold-change shrinkage for ranking and visualization GO Biological Process and KEGG pathway enrichment Full-cohort sensitivity analysis Committed figures and result tables Pinned software environment via renv GitHub Actions checks for environment consistency, linting, tests, and rebuild validation Main outputs Balanced primary analysis: 1,902 thresholded differentially expressed genes Full-cohort sensitivity analysis: 4,371 thresholded differentially expressed genes Shared thresholded genes: 1,314 Shared effect-direction concordance: 99.7% Reproducibility From the repository root: Rscript 000_install_dependencies.R Rscript run_all.R Rscript -e 'renv::status()' Rscript dev/lint.R Rscript -e 'testthat::test_dir("tests/testthat")' Positioning Relative to broader workflow standards, the repository includes pinned dependencies, deterministic seeds, committed derived outputs, CI rebuild checks, and explicit session provenance. It remains intentionally lightweight and reviewable, while leaving upstream FASTQ-level processing and covariate-rich modeling out of scope. Data source Lieberman NAP et al. (2020). In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biology 18(9): e3000849. GEO accession: GSE152075 DOI: https://doi.org/10.1371/journal.pbio.3000849