Cited by 945Single-cell and spatial transcriptomicsGenomics and Phylogenetic StudiesGene expression and cancer classification

Orchestrating single-cell analysis with Bioconductor

Open access
Amezquita, Robert A., Lun, Aaron T. L., Becht, Etienne, Carey, Vince J., Carpp, Lindsay N., Geistlinger, Ludwig, Marini, Federico, Rue-Albrecht, Kevin +9 more·2020·Nature Methods

Published version of a preprint

Abstract

Recent technological advancements have enabled the profiling of a large number of genome-wide features in individual cells. However, single-cell data present unique challenges that require the development of specialized methods and software infrastructure to successfully derive biological insights. The Bioconductor project has rapidly grown to meet these demands, hosting community-developed open-source software distributed as R packages. Featuring state-of-the-art computational methods, standardized data infrastructure and interactive data visualization tools, we present an overview and online book (https://osca.bioconductor.org) of single-cell methods for prospective users.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41592-019-0654-x

Cites

185 of 185 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Existing computational best practices and tool recommendations for scRNA-seq are outdated or incomplete.

    “although computational best practices and tool recommendations have previously been outlined for scRNA-seq2,5,6,17, they are either outdated or incomplete.”

    From Best practices for single-cell analysis across modalities (2023) · cites this paper as [2]

  • Removing cells with low total ADT count may remove cell types that do not express a specific set of proteins or express only a few.

    “however, removing cells with a low total ADT count may remove cell types that do not express a specific set of proteins or express only a few2.”

    From Best practices for single-cell analysis across modalities (2023) · cites this paper as [2]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., Waldron, L., Pagès, H., Smith, M. L., Huber, W., Morgan, M., Gottardo, R., & Hicks, S. C.
Affiliations
  • Fred Hutch Cancer Center (US)
  • Genentech (US)
  • Brigham and Women's Hospital (US)
  • City University of New York (US)
  • University of Padua (IT)
  • SIB Swiss Institute of Bioinformatics (CH)
  • European Molecular Biology Laboratory (DE)
  • Roswell Park Comprehensive Cancer Center (US)
  • Johns Hopkins University (US)
Corresponding author
Hicks, Stephanie C.
Venue
Nature Methods
Published
2019-12-02
Volume
17
Issue
2
Pages
137-145
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W2989807288
Cited by
945
References
185
Citations by year
2026: 129 · 2025: 179 · 2024: 192 · 2023: 185 · 2022: 113 · 2021: 97 · 2020: 46 · 2019: 4
FWCI
5.74
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Padua Research Archive (University of Padova) (submittedVersion, cc-by-nc-nd)
Funders
  • Silicon Valley Community Foundation (2018-183201)
  • Fred Hutchinson Cancer Research Center
  • Wellcome Trust (WT/108437/Z/15, 108437)
  • Chan Zuckerberg Initiative
  • Cancer Research UK (A17179)
  • European Commission (H2020, 633974)
  • Deutsche Forschungsgemeinschaft (GE3023/1-1, 031A537B, 01EO1003)
  • Bundesministerium für Bildung und Forschung (BMBF 01EO1003, 01EO1003, 031A537B)
  • German Network for Bioinformatics Infrastructure (031 A537B)
  • National Institutes of Health (01EO1003, H2020, 5u41hg004059-15)
  • Horizon 2020 Framework Programme (633974)
  • National Human Genome Research Institute (U41-HG004059, R00HG009007)
  • National Cancer Institute (U24CA180996, U24CA232979, U01CA214846)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Keywords
single-cell analysis, Bioconductor, R package, open source software, single-cell data visualization, single-cell RNA sequencing
MeSH terms
Software, Genome, Gene Expression Profiling, Single-Cell Analysis, High-Throughput Nucleotide Sequencing

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 ›

Are you an author, or do you see a problem with this page? Request a review