Title | Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. |
Publication Type | Journal Article |
Year of Publication | 2018 |
Authors | Van den Berge, Koen, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit, and Lieven Clement |
Journal | Genome Biol |
Volume | 19 |
Issue | 1 |
Pagination | 24 |
Date Published | 2018 Feb 26 |
ISSN | 1474-760X |
Keywords | Gene Expression Profiling, Sequence Analysis, RNA, Single-Cell Analysis, Software |
Abstract | Dropout events in single-cell RNA sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This has triggered the development of bespoke scRNA-seq DE methods to cope with zero inflation. Recent evaluations, however, have shown that dedicated scRNA-seq tools provide no advantage compared to traditional bulk RNA-seq tools. We introduce a weighting strategy, based on a zero-inflated negative binomial model, that identifies excess zero counts and generates gene- and cell-specific weights to unlock bulk RNA-seq DE pipelines for zero-inflated data, boosting performance for scRNA-seq. |
DOI | 10.1186/s13059-018-1406-4 |
Alternate Journal | Genome Biol |
Original Publication | Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. |
PubMed ID | 29478411 |
PubMed Central ID | PMC6251479 |
Grant List | ABS4NGS ANR-11-BINF-0001 / / Agence Nationale de la Recherche / International 1S 418 16N / / Fonds Wetenschappelijk Onderzoek / International U01 MH105979 / MH / NIMH NIH HHS / United States P7/06 / / IAP StUDyS grant / International 280032 / ERC_ / European Research Council / International U01 MH105979 / NH / NIH HHS / United States P01 CA142538 / CA / NCI NIH HHS / United States CA142538-08 / NH / NIH HHS / United States FK-16-107 / / Forschungskredit / International ERC-SMAC-290032 / ERC_ / European Research Council / International |
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