ArticleGenome biology2024
Library size confounds biology in spatial transcriptomics data.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.Nature methods · 2026Article
- KSTITCH links cellular morphology and gene expression in spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.Bioinformatics (Oxford, England) · 2026Article
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- SECTOR: structural entropy-based learning of spatiotemporal organisation in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
- Benchmarking sketching methods on spatial transcriptomics data.Nucleic acids research · 2026Article
- A comprehensive survey of computer vision methods for spatial transcriptomics.Briefings in bioinformatics · 2026Review
- Advances in Spatial Transcriptomics in Bone.Current osteoporosis reports · 2026Review
- From glycolytic signatures to patients: A translational roadmap for reproducible, equitable deployment of multi-omics and AI in colorectal cancer.Medical oncology (Northwood, London, England) · 2026Article
- DeepSpaceDB: a spatial transcriptomics atlas for interactive in-depth analysis of tissues and tissue microenvironments.Nucleic acids research · 2026Article
- SCALE: unsupervised multiscale domain identification in spatial omics data.Nucleic acids research · 2026Article
- Graph Topology Reframes the Coherence of Cell-State Manifold Inference under Heterogeneous Single-Cell Observations.Computational and structural biotechnology journal · 2026Article
- From Raw Data to Biological Insights: A Practical Guide for Spatial Transcriptomics Analysis in R and Python.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts.European journal of immunology · 2026Article
- Randomized Spatial PCA (RASP): A computationally efficient method for dimensionality reduction of high-resolution spatial transcriptomics data.PLoS computational biology · 2025Article
- Decrypting cancer's spatial code: from single cells to tissue niches.Molecular oncology · 2025Review
- A deep learning-based multiscale integration of spatial omics with tumor morphology.Nature communications · 2025Article
- scGALA advances graph link prediction-based cell alignment for comprehensive data integration and harmonization.Nature communications · 2025Article
- Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools including normalization methods. Here, we demonstrate that library size is associated with tissue structure and that normalizing these effects out using commonly applied scRNA-seq normalization methods will negatively affect spatial domain identification. Spatial data should not be specifically corrected for library size prior to analysis, and algorithms designed for scRNA-seq data should be adopted with caution.
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Registered trials
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.