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. The workflow implements an end-to-end pipeline: FASTQ quality control (FastQC, MultiQC) Optional read trimming (Cutadapt) STARsolo alignment and gene–cell count matrix generation Seurat-based quality control, normalization, feature selection, clustering, and annotation Pseudobulk differential expression analysis using DESeq2 Two one-sided tests (TOST) for equivalence testing Gene set enrichment analysis (GSEA / ORA) Cell-type–specific co-expression network construction and module enrichment Execution is managed via Snakemake and Docker to ensure reproducibility and environment consistency. The repository associated with this record contains the complete workflow definition and container configuration. Contents of Version 2.0.0 This version provides a lightweight demonstration bundle designed to validate workflow execution: A chromosome 1 (chr1) GRCh38 mini-reference A pre-built STAR index for chr1 A reduced FASTQ subset (~100,000 reads) Representative pipeline outputs from a full PBMC run The toy dataset is intended for rapid testing and reproducibility verification. It runs in approximately 5–10 minutes on a standard workstation after container setup and demonstrates upstream processing through Seurat object creation. 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.数据集描述 本数据集提供了一套可复现、容器化的外周血单个核细胞（peripheral blood mononuclear cell, PBMC）单细胞RNA测序（single-cell RNA-seq, scRNA-seq）数据分析工作流。 该工作流实现了端到端的分析管线： - FASTQ质量控制（FastQC、MultiQC） - 可选读段修剪（Cutadapt） - STARsolo比对与基因-细胞计数矩阵生成 - 基于Seurat的质量控制、归一化、特征选择、聚类与注释 - 采用DESeq2的伪批量差异表达分析 - 用于等效性检验的双单侧检验（Two one-sided tests, TOST） - 基因集富集分析（Gene Set Enrichment Analysis, GSEA / 过表达富集分析(Over-Representation Analysis, ORA)） - 细胞类型特异性共表达网络构建与模块富集分析 流程执行通过Snakemake与Docker进行管控，以保障可复现性与运行环境的一致性。本数据集关联的代码仓库包含完整的工作流定义与容器配置文件。 ## 2.0.0版内容 本版本提供了轻量化演示套件，用于验证工作流的执行： - 1号染色体（chr1）的GRCh38迷你参考基因组 - 针对chr1的预构建STAR比对索引 - 缩减后的FASTQ读段子集（约100,000条读段） - 完整PBMC测序运行的代表性管线输出结果 该玩具数据集旨在用于快速测试与可复现性验证。完成容器搭建后，可在标准工作站上于5至10分钟内完成运行，可演示从上游处理至Seurat对象创建的完整流程。 ## 可复现性说明 由于文件体积限制，本归档包未包含完整的GRCh38参考基因组与注释文件。用于复现完整分析所需的精准参考数据源、版本信息与配置细节，已在关联的GitHub代码仓库中完成文档说明。 完整的工作流（包含配置文件、容器定义与执行说明）可通过以下网址获取： https://github.com/Inkasimo/scRNAseq-pbmc-workflow 本版本为演示数据与对应标记版本软件发布的代表性分析结果的稳定快照。