ArticleNAR genomics and bioinformatics2020
Comparison of visualization tools for single-cell RNAseq data.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
44 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data.Nucleic acids research · 2025Pooled it
- Meta-Analysis of Human Cancer Single-Cell RNA-Seq Datasets Using the IMMUcan Database.Cancer research · 2023Pooled it
- anndataR improves interoperability between R and Python in single-cell transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Metabolic adaptations rewire CD4Nature immunology · 2026Article
- BDCD: a comprehensive Brain Disease Cell-cell communication Database.Database : the journal of biological databases and curation · 2026Article
- Multi-Omics and Single-Cell Dissection Reveals EXT1 as a Glycosylation-Linked Therapeutic Target in Cancer.Oncology research · 2026Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution.The Journal of physiology · 2025Article
- Analysis of individual patient pathway coordination in a cross-species single-cell kidney atlas.Nature genetics · 2025Article
- Joint representation and visualization of derailed cell states with Decipher.Genome biology · 2025Article
- Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.Cell genomics · 2025Article
- Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics.Science advances · 2025Article
- Infusing structural assumptions into dimensionality reduction for single-cell RNA sequencing data to identify small gene sets.Communications biology · 2025Article
- paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host-parasite single-cell RNA-seq data.Nucleic acids research · 2025Article
- Integration of multi-omics and single-cell transcriptome reveals mitochondrial outer membrane protein-2 (MTX-2) as a prognostic biomarker and characterizes ubiquinone metabolism in lung adenocarcinoma.Journal of Cancer · 2025Article
- Multi-omics profiling reveals PLEKHA6 as a modulator of β-catenin signaling and therapeutic vulnerability in lung adenocarcinoma.American journal of cancer research · 2025Article
- easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis.Bioinformatics (Oxford, England) · 2024Article
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- Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
In the last decade, single cell RNAseq (scRNAseq) datasets have grown in size from a single cell to millions of cells. Due to its high dimensionality, it is not always feasible to visualize scRNAseq data and share it in a scientific report or an article publication format. Recently, many interactive analysis and visualization tools have been developed to address this issue and facilitate knowledge transfer in the scientific community. In this study, we review several of the currently available scRNAseq visualization tools and benchmark the subset that allows to visualize the data on the web and share it with others. We consider the memory and time required to prepare datasets for sharing as the number of cells increases, and additionally review the user experience and features available in the web interface. To address the problem of format compatibility we have also developed a user-friendly R package,
Identifiers
What OpenQuestion holds
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.