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Single-cell RNA-seq Analysis — scRNA-seq

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.

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Sources

  1. 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. DOI: 10.1038/nbt.3192 ↗
  2. Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., ... & McCarroll, S. A. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell, 161(5), 1202–1214. DOI: 10.1016/j.cell.2015.05.002 ↗

Related methods

Gene Set Enrichment AnalysisPathway Enrichment AnalysisRNA-seq Differential ExpressionSingle-cell eQTL analysisSingle-cell variant calling

Referenced by

Bayesian RNA-seq differential expressionChIP-seq Peak CallingDifferential single-cell RNA-seq analysiseQTL AnalysisGene Set Enrichment AnalysisMachine learning-assisted ChIP-seq peak callingMachine learning-assisted gene set enrichment analysisMachine learning-assisted RNA-seq differential expressionMachine learning-assisted single-cell RNA-seq analysisMulti-omics single-cell RNA-seq analysisNetwork-based RNA-seq differential expressionNetwork-based single-cell RNA-seq analysisPathway Enrichment AnalysisRNA-seq Differential ExpressionSequence AlignmentSingle-cell ChIP-seq peak callingSingle-cell Copy Number Variation AnalysisSingle-cell eQTL analysisSingle-cell Gene Set Enrichment AnalysisSingle-cell GWASSingle-cell metabolomics analysisSingle-cell Microbiome Diversity AnalysisSingle-cell Phylogenetic AnalysisSingle-cell RNA-seq differential expressionTime-series gene set enrichment analysisTime-series microbiome diversity analysisTime-series RNA-seq differential expressionTime-series single-cell RNA-seq analysis

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ScholarGate — Single-cell RNA-seq analysis (Single-cell RNA Sequencing Analysis). Retrieved 2026-06-04 from https://scholargate.app/tr/bioinformatics/single-cell-rna-seq-analysis