BEARscc (Bayesian ERCC Assessment of Robustness of Single Cell Clusters) is a tool to assess single-cell RNA-seq clusters. The BEARscc algorithm estimates experimental noise using ERCC spike-in controls.
Transcriptomics; RNA-seq
Severson DT, Owen RP, White MJ, Lu X, Schuster-Bockler B "BEARscc determines robustness of single-cell clusters using simulated technical replicates." Nat Commun. 2018 Mar 22;9(1):1187. https://doi.org/10.1038/s41467-018-03608-y
PMID: 29567991
PMCID: PMC5864873
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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