方法对比

	RNA-seq差异表达	Single-cell RNA-seq analysis
领域	生物信息学	生物信息学
方法族	Process / pipeline	Process / pipeline
起源年份	2008–2010 (RNA-seq DE methodology established)	2009 (first scRNA-seq by Tang et al.); widely adopted 2015–2016
提出者	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)	Azim Surani, Barbara Treutlein, and the Regev/McCarroll groups (foundational droplet-based methods ~2015)
类型	Quantitative genomics pipeline	High-throughput single-cell transcriptomic profiling pipeline
开创性文献	Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.	Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nature Biotechnology, 33(5), 495–502.
别名	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA	scRNA-seq, single-cell transcriptomics, scRNAseq analysis, single-cell gene expression profiling
相关	6	5
摘要	RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values.	Single-cell RNA sequencing (scRNA-seq) analysis characterises gene expression at the resolution of individual cells, enabling discovery of cell types, states, and transitions that are invisible in bulk transcriptomics. Starting from raw sequencing reads, the workflow produces a cell-by-gene count matrix and proceeds through quality control, normalisation, dimensionality reduction, unsupervised clustering, cell-type annotation, and a range of downstream analyses such as trajectory inference and differential expression between cell populations.