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	Single-cell eQTL-analys	RNA-seq Differential Expression
Ämnesområde	Bioinformatik	Bioinformatik
Familj	Process / pipeline	Process / pipeline
Ursprungsår	2020	2008–2010 (RNA-seq DE methodology established)
Upphovsperson	Cuomo et al.; Kim-Hellmuth et al. (pioneering sc-eQTL frameworks, 2020)	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Typ	Statistical genomics pipeline	Quantitative genomics pipeline
Ursprungskälla	Cuomo, A. S. E., et al. (2020). Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nature Communications, 11(1), 810.	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.
Alias	sc-eQTL analysis, single-cell eQTL mapping, scRNA-seq eQTL, cell-type-specific eQTL	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Närliggande	6	6
Sammanfattning	Single-cell eQTL analysis identifies genetic variants (eQTLs) that regulate gene expression in a cell-type-specific manner by jointly analysing single-cell RNA-seq profiles and donor genotype data. Unlike bulk eQTL methods, it resolves regulatory effects that are diluted or masked when cell types are mixed, enabling discovery of variants whose effects are confined to particular cell states or developmental stages.	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.