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Cited by 828

The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.

Trajectory-based differential expression analysis for single-cell sequencing data

Open access
Van den Berge, Koen, Roux de Bézieux, Hector, Street, Kelly, Saelens, Wouter, Cannoodt, Robrecht, Saeys, Yvan, Dudoit, Sandrine, Clement, Lieven·2020·Nature Communications
DOI 10.1038/s41467-020-14766-3

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Abstract

Trajectory inference has radically enhanced single-cell RNA-seq research by enabling the study of dynamic changes in gene expression. Downstream of trajectory inference, it is vital to discover genes that are (i) associated with the lineages in the trajectory, or (ii) differentially expressed between lineages, to illuminate the underlying biological processes. Current data analysis procedures, however, either fail to exploit the continuous resolution provided by trajectory inference, or fail to pinpoint the exact types of differential expression. We introduce tradeSeq, a powerful generalized additive model framework based on the negative binomial distribution that allows flexible inference of both within-lineage and between-lineage differential expression. By incorporating observation-level weights, the model additionally allows to account for zero inflation. We evaluate the method on simulated datasets and on real datasets from droplet-based and full-length protocols, and show that it yields biological insights through a clear interpretation of the data.

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Show all 11 references

Research works printed but not linked: 31

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Cited by

Metadata

Authors
Van den Berge, K., Roux de Bézieux, H., Street, K., Saelens, W., Cannoodt, R., Saeys, Y., Dudoit, S., & Clement, L.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2020-03-05
Volume
11
Issue
1
Pages
1201-1201
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-020-14766-3
OpenAlex
W3009370296
Cited by
828
References
11
FWCI
22.89
Type
journal article
Language
en
Open access
gold
Licence
Funders
  • Belgian American Educational Foundation
  • Fonds Wetenschappelijk Onderzoek (G062219N, 1246220N, 148095)

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