ArticleNature communications2019
A systematic evaluation of single cell RNA-seq analysis pipelines.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 papers, 1 of them a synthesis that pooled it.
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Who cites it
143 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Beyond the mean: genetic control of gene expression fidelity and dispersion.bioRxiv : the preprint server for biology · 2026Article
- Multimodal single cell analyses reveal gene networks of planarian stem cell differentiation.Nature communications · 2025Article
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- SmartImpute is a targeted imputation framework for single-cell transcriptome data.Cell reports methods · 2025Article
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- The Dyson equalizer: adaptive noise stabilization for low-rank signal detection and recovery.Information and inference : a journal of the IMA · 2025Article
- Single-Cell Sequencing: Genomic and Transcriptomic Approaches in Cancer Cell Biology.International journal of molecular sciences · 2025Review
- Laser-capture microdissection for spatial transcriptomics of immunohistochemically detected neurons.The Journal of biological chemistry · 2025Article
- Single-cell sequencing in diabetic retinopathy: progress and prospects.Journal of translational medicine · 2025Review
- Considerations for building and using integrated single-cell atlases.Nature methods · 2025Review
- Uncovering functional lncRNAs by scRNA-seq with ELATUS.Nature communications · 2024Article
- An AI Agent for Fully Automated Multi-Omic Analyses.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.NAR genomics and bioinformatics · 2024Article
- Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data.Genomics, proteomics & bioinformatics · 2024Article
- Single-Cell Sequencing: High-Resolution Analysis of Cellular Heterogeneity in Autoimmune Diseases.Clinical reviews in allergy & immunology · 2024Review
- scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.bioRxiv : the preprint server for biology · 2024Article
83 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The recent rapid spread of single cell RNA sequencing (scRNA-seq) methods has created a large variety of experimental and computational pipelines for which best practices have not yet been established. Here, we use simulations based on five scRNA-seq library protocols in combination with nine realistic differential expression (DE) setups to systematically evaluate three mapping, four imputation, seven normalisation and four differential expression testing approaches resulting in ~3000 pipelines, allowing us to also assess interactions among pipeline steps. We find that choices of normalisation and library preparation protocols have the biggest impact on scRNA-seq analyses. Specifically, we find that library preparation determines the ability to detect symmetric expression differences, while normalisation dominates pipeline performance in asymmetric DE-setups. Finally, we illustrate the importance of informed choices by showing that a good scRNA-seq pipeline can have the same impact on detecting a biological signal as quadrupling the sample size.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.