CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an R tool to classify cells in single-cell RNA-seq datasets. The CHETAH algorithm uses a reference dataset and hierarchical clustering of reference data to compute a tree for top-to-bottom classification.
Gene expression; RNA-seq
de Kanter JK, Lijnzaad P, Candelli T, Margaritis T, Holstege FCP "CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing." Nucleic Acids Res. 2019 Sep 19;47(16):e95. https://doi.org/10.1093/nar/gkz543
PMID: 31226206
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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