ArticleCell systems2018
Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A time-resolved meta-analysis of consensus gene expression profiles during human T-cell activation.Genome biology · 2023Pooled it
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- Galectin and Myc enable cochlear progenitor expansion in vitro and in vivo.bioRxiv : the preprint server for biology · 2026Article
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- A Multimodal Spatial and Epigenomic Atlas of Human Adult Lung Topography.bioRxiv : the preprint server for biology · 2025Article
- A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics.Nature communications · 2025Article
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- Exploring RNA-Seq Data Analysis Through Visualization Techniques and Tools: A Systematic Review of Opportunities and Limitations for Clinical Applications.Bioengineering (Basel, Switzerland) · 2025Review
- Single-cell transcriptomic atlas reveals increased regeneration in diseased human inner ear balance organs.Nature communications · 2024Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- Clinical implications of single cell sequencing for bladder cancer.Oncology research · 2024Review
- Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.Nature protocols · 2023Review
- Essential procedures of single-cell RNA sequencing in multiple myeloma and its translational value.Blood science (Baltimore, Md.) · 2023Review
- An introduction to representation learning for single-cell data analysis.Cell reports methods · 2023Review
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- SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance.Nature communications · 2023Article
- Apoptotic cell fragments locally activate tingible body macrophages in the germinal center.Cell · 2023Article
- Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma.bioRxiv : the preprint server for biology · 2023Article
- Using Global t-SNE to Preserve Intercluster Data Structure.Neural computation · 2022Article
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Abstract
High-throughput single-cell gene expression profiling has enabled the definition of new cell types and developmental trajectories. Visualizing these datasets is crucial to biological interpretation, and a popular method is t-stochastic neighbor embedding (t-SNE), which visualizes local patterns well but distorts global structure, such as distances between clusters. We developed similarity weighted nonnegative embedding (SWNE), which enhances interpretation of datasets by embedding the genes and factors that separate cell states on the visualization alongside the cells and maintains fidelity when visualizing local and global structure for both developmental trajectories and discrete cell types. SWNE uses nonnegative matrix factorization to decompose the gene expression matrix into biologically relevant factors; embeds the cells, genes, and factors in a 2D visualization; and uses a similarity matrix to smooth the embeddings. We demonstrate SWNE on single-cell RNA-seq data from hematopoietic progenitors and human brain cells. SWNE is available as an R package at github.com/yanwu2014/swne.
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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.