ArticleF1000Research2020
clustifyr: an R package for automated single-cell RNA sequencing cluster classification.
Article in F1000Research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed.
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- celltypeEnrich: a consensus-based scRNA-seq cluster annotation tool.bioRxiv : the preprint server for biology · 2026Article
- Monocytic niches escape T cell surveillance and promote Mycobacterium tuberculosis persistence in lymph nodes.Immunity · 2026Article
- Single-nucleus transcriptomics-based drug screening platform for focal cortical dysplasia.Molecular psychiatry · 2026Article
- Chikungunya virus persists in joint-associated macrophages and promotes chronic disease in mice.Nature microbiology · 2026Article
- ICON: An isoform-aware hierarchical random forest model for cell type classification.bioRxiv : the preprint server for biology · 2026Article
- Review
- Transcriptomics- and 3D imaging-based characterization of the lymphatic vasculature in human skin.The Journal of experimental medicine · 2026Article
- Autologous human iPSC-derived alveolus-on-chip reveals early pathological events ofScience advances · 2026Article
- USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens.PLoS biology · 2025Article
- Type I IFN drives neutrophil swarming, impeding lung T cell-macrophage interactions and TB control.The Journal of experimental medicine · 2025Article
- An inflammatory T-cell-stromal axis contributes to hematopoietic stem/progenitor cell failure and clonal evolution in human myelodysplastic syndrome.Nature communications · 2025Article
- Heterozygous pathogenic variants in the splicing factor SF1 lead to a large spectrum of neurodevelopmental disorders.American journal of human genetics · 2025Article
- Multi-pronged analysis of pediatric low-grade glioma and ganglioglioma reveals a unique tumor microenvironment associated with BRAF alterations.Brain pathology (Zurich, Switzerland) · 2025Article
- Automated classification of cellular expression in multiplexed imaging data with Nimbus.Nature methods · 2025Article
- A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes.Nature communications · 2025Article
- Spatial gene expression at single-cell resolution from histology using deep learning with GHIST.Nature methods · 2025Article
- IL7RBrain and behavior · 2025Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expression profiles to assign likely cell types using data from scRNA-seq, bulk RNA-seq, microarray expression data, or signature gene lists. We benchmark various parameters of a correlation-based approach and implement gene list enrichment methods. clustifyr is a lightweight and effective cell-type assignment tool developed for compatibility with various scRNA-seq analysis workflows. clustifyr is publicly available at https://github.com/rnabioco/clustifyr.
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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.