ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data Article Swipe
Davide Risso
,
Fanny Perraudeau
,
Svetlana Gribkova
,
Sandrine Dudoit
,
Jean‐Philippe Vert
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1101/125112
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1101/125112
Single-cell RNA sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data. We demonstrate, with simulated and real data, that the model and its associated estimation procedure are able to give a more stable and accurate low-dimensional representation of the data than principal component analysis (PCA) and zero-inflated factor analysis (ZIFA), without the need for a preliminary normalization step.
Related Topics
Concepts
Normalization (sociology)
Negative binomial distribution
Principal component analysis
RNA-Seq
Computer science
Count data
Algorithm
Mathematics
Computational biology
Statistics
Pattern recognition (psychology)
Gene
Biology
Artificial intelligence
Transcriptome
Genetics
Gene expression
Sociology
Poisson distribution
Anthropology
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/125112
- https://www.biorxiv.org/content/biorxiv/early/2017/11/02/125112.full.pdf
- OA Status
- green
- Cited By
- 41
- References
- 61
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2606690922
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2606690922Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/125112Digital Object Identifier
- Title
-
ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq dataWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2017Year of publication
- Publication date
-
2017-04-06Full publication date if available
- Authors
-
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean‐Philippe VertList of authors in order
- Landing page
-
https://doi.org/10.1101/125112Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2017/11/02/125112.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2017/11/02/125112.full.pdfDirect OA link when available
- Concepts
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Normalization (sociology), Negative binomial distribution, Principal component analysis, RNA-Seq, Computer science, Count data, Algorithm, Mathematics, Computational biology, Statistics, Pattern recognition (psychology), Gene, Biology, Artificial intelligence, Transcriptome, Genetics, Gene expression, Sociology, Poisson distribution, AnthropologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
41Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1, 2023: 5, 2022: 2, 2021: 5, 2020: 1Per-year citation counts (last 5 years)
- References (count)
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61Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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