Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference Article Swipe
Fanny Perraudeau
,
Davide Risso
,
Kelly Street
,
Elizabeth Purdom
,
Sandrine Dudoit
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.12122.1
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.12122.1
Novel single-cell transcriptome sequencing assays allow researchers to measure gene expression levels at the resolution of single cells and offer the unprecendented opportunity to investigate at the molecular level fundamental biological questions, such as stem cell differentiation or the discovery and characterization of rare cell types. However, such assays raise challenging statistical and computational questions and require the development of novel methodology and software. Using stem cell differentiation in the mouse olfactory epithelium as a case study, this integrated workflow provides a step-by-step tutorial to the methodology and associated software for the following four main tasks: (1) dimensionality reduction accounting for zero inflation and over dispersion and adjusting for gene and cell-level covariates; (2) cell clustering using resampling-based sequential ensemble clustering; (3) inference of cell lineages and pseudotimes; and (4) differential expression analysis along lineages.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.12688/f1000research.12122.1
- https://f1000research.com/articles/6-1158/v1/pdf
- OA Status
- gold
- Cited By
- 16
- References
- 11
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2737169389
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2737169389Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.12688/f1000research.12122.1Digital Object Identifier
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Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inferenceWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2017Year of publication
- Publication date
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2017-07-21Full publication date if available
- Authors
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Fanny Perraudeau, Davide Risso, Kelly Street, Elizabeth Purdom, Sandrine DudoitList of authors in order
- Landing page
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https://doi.org/10.12688/f1000research.12122.1Publisher landing page
- PDF URL
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https://f1000research.com/articles/6-1158/v1/pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://f1000research.com/articles/6-1158/v1/pdfDirect OA link when available
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Bioconductor, Computational biology, Biology, Cluster analysis, Dimensionality reduction, Transcriptome, Inference, Computer science, Data mining, Bioinformatics, Gene, Gene expression, Genetics, Artificial intelligenceTop concepts (fields/topics) attached by OpenAlex
- Cited by
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16Total citation count in OpenAlex
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2024: 1, 2022: 2, 2021: 2, 2020: 3, 2019: 2Per-year citation counts (last 5 years)
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11Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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