SC3: consensus clustering of single-cell RNA-seq data
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Abstract
Single-cell RNA-seq enables the quantitative characterization of cell types based on global transcriptome profiles. We present single-cell consensus clustering (SC3), a user-friendly tool for unsupervised clustering, which achieves high accuracy and robustness by combining multiple clustering solutions through a consensus approach (http://bioconductor.org/packages/SC3). We demonstrate that SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.
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SC3 separated microglia into four clusters, whereby 99.8% of 5xFAD XO4+ cells and 99.2% of WT 6 m microglia were entirely contained within Clusters 2 and 3, respectively.
“Single-cell consensus clustering (SC3)40 separated microglia into four clusters, whereby 99.8% of 5xFAD XO4+ cells and 99.2% of WT 6 m microglia were entirely contained within Clusters 2 and 3, respectively”
From Transcriptional signature in microglia associated with Aβ plaque phagocytosis (2021) · cites this paper as [40]
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- Authors
- Kiselev, V. Y., Kirschner, K., Schaub, M. T., Andrews, T., Yiu, A., Chandra, T., Natarajan, K. N., Reik, W., Barahona, M., Green, A. R., & Hemberg, M.
- Affiliations
- Wellcome Sanger Institute (GB)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- University of Namur (BE)
- Babraham Institute (GB)
- European Bioinformatics Institute (GB)
- Imperial College London (GB)
- Corresponding author
- Hemberg, Martin
- ORCID
- Venue
- Nature Methods
- Published
- 2017-03-27
- Volume
- 14
- Issue
- 5
- Pages
- 483-486
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC5410170
- OpenAlex
- W2598326928
- Cited by
- 1,500
- References
- 14
- Citations by year
- 2026: 73 · 2025: 126 · 2024: 169 · 2023: 174 · 2022: 185 · 2021: 235 · 2020: 211 · 2019: 161 · 2018: 123 · 2017: 37 · 2016: 3 · 2014: 1 · 2012: 1
- FWCI
- 60.12
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- DIAL (Catholic University of Leuven) (submittedVersion)
- Digital Access to Libraries (Université catholique de Louvain (UCL), l'Université de Namur (UNamur) and the Université Saint-Louis (USL-B)) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Leukemia and Lymphoma Society
- Wellcome Trust (104710, 104710/Z/14/Z, 098051)
- Cancer Research UK (21762)
- National Institute for Health and Care Research
- Kay Kendall Leukaemia Fund
- Blood Cancer UK (07037)
- Medical Research Council (MC_PC_12009)
- Engineering and Physical Sciences Research Council (EP/N014529/1)
- Biotechnology and Biological Sciences Research Council (BB/K010867/1, BBS/E/B/000C0426)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- single-cell RNA sequencing, cell clustering, consensus clustering, unsupervised clustering, cell type annotation, neoplastic cells, Bioconductor package
- MeSH terms
- Hematopoietic Stem Cells, Humans, Cluster Analysis, Sequence Analysis, RNA, Gene Expression Profiling, Single-Cell Analysis, High-Throughput Nucleotide Sequencing, Support Vector Machine, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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