clusterExperiment is a tool for clustering single-cell RNA-seq data. The clusterExperiment algorithm uses the Resampling-based Sequential Ensemble Clustering (RSEC) method for the creation of various user-defined clusters and computation of a consensus cluster. The package also contains visualization tools and functions for the detection of cluster signatures.
Sequencing; RNA-seq
Risso D, Purvis L, Fletcher RB, Das D, Ngai J, Dudoit S, Purdom E "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets." PLoS Comput Biol. 2018 Sep 4;14(9):e1006378. eCollection 2018 Sep. https://doi.org/10.1371/journal.pcbi.1006378
PMID: 30180157
PMCID: PMC6138422
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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