Reproducible scRNA-seq PBMC Workflow: Reference, Toy Demonstration Data, and Analysis Outputs

Description This record provides a reproducible, containerized single-cell RNA-seq (scRNA-seq) workflow for peripheral blood mononuclear cell (PBMC) data analysis. Execution is managed via Snakemake and Docker to ensure environment consistency. Workflow Capabilities The integrated pipeline implements an end-to-end orchestration: Upstream: FASTQ QC (FastQC/MultiQC), Optional Trimming (Cutadapt), and STARsolo alignment. Downstream: Seurat-based clustering/annotation, Pseudobulk DESeq2, TOST equivalence testing, GSEA/ORA, and Cell-type–specific co-expression networks (MUUMI). Contents of Version 3.0.0 This version provides a validation suite and a representative result archive (~6 GB): Toy Demonstration Bundle: A chromosome 1 (chr1) mini-reference, pre-built STAR index, and a reduced FASTQ subset (~100,000 reads) for rapid 5–10 minute execution testing. Full Result Archive: Representative execution artifacts from the 4-donor PBMC dataset, including STARsolo gene-cell matrices, Seurat objects, TOST equivalence tables, and MUUMI co-expression networks. The toy dataset validates the orchestration engine through Seurat object creation, while the included results archive provides the technical provenance for the full downstream analysis. Reproducibility Notes The full GRCh38 reference genome and annotation files are not included in this archive due to size. Exact reference sources, versions, and configuration details required to reproduce the full analysis are documented in the associated GitHub repository. The complete workflow, including configuration, container definition, and execution instructions, is available at: https://github.com/Inkasimo/scRNAseq-pbmc-workflow This version reflects a stable snapshot of the demonstration data and representative analysis outputs aligned with the corresponding tagged software release.