ZINB-WaVE is a tool to produce low-dimensional representations of single-cell RNA-seq data sets. The ZINB-WaVE algorithm uses a zero-inflated negative binomial model that estimates zero inflation (dropouts), over-dispersion, and the counts. It also considers varied library sizes and covariates, that eliminates the need to normalize data.
Gene expression; RNA-seq; Sequencing; Transcriptomics
Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP "A general and flexible method for signal extraction from single-cell RNA-seq data." Nat Commun. 2018 Jan 18;9(1):284. https://doi.org/10.1038/s41467-017-02554-5
PMID: 29348443
PMCID: PMC5773593
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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