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CHETAH

CHETAH

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.

Topic

Gene expression; RNA-seq

Details

  • Operation: RNA-Seq analysis; Classification
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: GNU Affero General Public License v3.0
  • Cost: Free
  • Version name: 1.2.0
  • Maturity: Stable
  • Credit: European Research Council (ERC), KIKA.
  • Contact: Jurrian de Kanter jurriandekanter _at_ gmail.com | Philip Lijnzaad Lijnzaad
  • Collection: Bioconductor

Publications

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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