ArticleComputational and structural biotechnology journal2020
Benchmarking algorithms for pathway activity transformation of single-cell RNA-seq data.
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- PathwayBench: a multi-criterion benchmark of pseudobulk pathway activity scoring methods reveals rank-window competition as a mechanism of biological signal loss in single-cell RNA-seq.Research square · 2026Article
- Interpretable and scalable spatial gene set activity analysis with GESSO uncovers functional tissue architecture.bioRxiv : the preprint server for biology · 2026Article
- Decoding apoptosis, ferroptosis, and inflammatory cell death in adenomyosis at single-cell resolution.Briefings in bioinformatics · 2026Article
- PathwayEmbed: a computational tool to quantify intracellular signaling transduction states from transcriptomic data.Bioinformatics (Oxford, England) · 2026Article
- scResponse: A Rank-Based Method for Identifying Cell States That Contribute to Immunotherapy Response by Single-Cell Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RAS pathway activity subtypes identified by machine learning define prognostic and immune microenvironment characteristics in lung adenocarcinoma.Discover oncology · 2026Article
- Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.Nature aging · 2026Article
- FUNCellA: A Tool for Single-Sample Enrichment Analysis and Relative Pathway Activity Estimation in Single-Cell RNA Sequencing Data.Computational and structural biotechnology journal · 2026Article
- Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.Cancer metastasis reviews · 2025Review
- The kinase ERK plays a conserved dominant role in the heterogeneity of epithelial-mesenchymal transition in pancreatic cancer cells.Science signaling · 2025Article
- Integrating microbial GWAS and single-cell transcriptomics reveals associations between host cell populations and the gut microbiome.Nature microbiology · 2025Article
- Applying integrated transcriptome and single-cell sequencing analysis to develop a prognostic signature based on M2-like tumor-associated macrophages for breast cancer.Discover oncology · 2025Article
- Systematic dissection of pleiotropic loci and critical regulons in excitatory neurons and microglia relevant to neuropsychiatric and ocular diseases.Translational psychiatry · 2025Article
- Spatial Transcriptomic Analyses of Spermatogenesis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure.Nature communications · 2024Article
- Comparative analysis of single-cell pathway scoring methods and a novel approach.NAR genomics and bioinformatics · 2024Article
- Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue.Genome research · 2024Article
- Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data.Genomics, proteomics & bioinformatics · 2024Article
- Beyond benchmarking and towards predictive models of dataset-specific single-cell RNA-seq pipeline performance.Genome biology · 2024Article
- A map of signaling responses in the human airway epithelium.Cell systems · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biological pathway analysis provides new insights for cell clustering and functional annotation from single-cell RNA sequencing (scRNA-seq) data. Many pathway analysis algorithms have been developed to transform gene-level scRNA-seq data into functional gene sets representing pathways or biological processes. Here, we collected seven widely-used pathway activity transformation algorithms and 32 available datasets based on 16 scRNA-seq techniques. We proposed a comprehensive framework to evaluate their accuracy, stability and scalability. The assessment of scRNA-seq preprocessing showed that cell filtering had the less impact on scRNA-seq pathway analysis, while data normalization of sctransform and scran had a consistent well impact across all tools. We found that Pagoda2 yielded the best overall performance with the highest accuracy, scalability, and stability. Meanwhile, the tool PLAGE exhibited the highest stability, as well as moderate accuracy and scalability.
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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.