ReviewGenome biology2021
Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape.
Review in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- SC-framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets.iScience · 2026Article
- Single-Cell Omics Advances in Understanding Tissue Development and Complex Trait Formation in Sheep and Goats.Animals : an open access journal from MDPI · 2026Review
- Classification of indeterminate and off-target cell types within human kidney organoid differentiation.iScience · 2026Article
- A unified single-cell atlas of HNSCC: Toward characterizing HPV- and sex-associated TME variability.iScience · 2026Article
- Exploring specialized metabolic pathways in medicinal plants with single-cell and spatial omics.Acta pharmaceutica Sinica. B · 2026Review
- Pitfalls in analysis and interpretation of single-cell RNA-seq data in cancer.Neuro-oncology advances · 2026Review
- A multi-agent platform for assessment and improvement of bioinformatics software documentation.bioRxiv : the preprint server for biology · 2026Article
- SCSEQ: A web tool for analyzing single-cell RNA-seq data.GigaScience · 2026Article
- Single Cell RNA Sequencing in Colorectal Cancer Immunology: Recent Updates, Application, and Emerging Challenges.Current molecular medicine · 2026Review
- SCpubr: a user-friendly R-package for generating publication-ready visualizations of single-cell transcriptome analyses.Bioinformatics advances · 2026Article
- Immune regulation and therapeutic targets in sepsis: insights from single-cell transcriptomics.Frontiers in immunology · 2026Review
- Exploring immune modulation in osteoarthritis: identifying key biomarkers and the role of PTPRC in regulating immune microenvironment for therapeutic intervention.Frontiers in immunology · 2026Article
- Multimodal learning enables chat-based exploration of single-cell data.Nature biotechnology · 2025Article
- Tumour Single-Cell Bioinformatics: From Immune Profiling to Molecular Dynamics.Journal of cellular and molecular medicine · 2025Review
- Catalyzing computational biology research at an academic institute through an interest network.PLoS computational biology · 2025Article
- The current landscape and emerging challenges of benchmarking single-cell methods.Briefings in bioinformatics · 2025Review
- A message passing framework for precise cell state identification with scClassify2.Genome biology · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent years have seen a revolution in single-cell RNA-sequencing (scRNA-seq) technologies, datasets, and analysis methods. Since 2016, the scRNA-tools database has cataloged software tools for analyzing scRNA-seq data. With the number of tools in the database passing 1000, we provide an update on the state of the project and the field. This data shows the evolution of the field and a change of focus from ordering cells on continuous trajectories to integrating multiple samples and making use of reference datasets. We also find that open science practices reward developers with increased recognition and help accelerate the field.
Indexed as
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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.