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cellTree

cellTree

a Latent Dirichlet Allocation (LDA) model

Topic

RNA-Seq; Cell biology; Data visualisation

Details

  • Operation: Sequence visualisation
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 1.16.0
  • Maturity: Mature
  • Credit: JST CREST, Grant-in-Aid for JSPS Fellows, Grant-in-Aid for Young Scientists, Grant-in-Aid for Scientific Research on Innovative Areas, JST ERATO, RIKEN, NIMS MI2I, Kakenhi Nanostructure and Kakenhi.
  • Contact: David A. duVerle dave _at_ cb.k.u-tokyo.ac.jp
  • Collection: Bioconductor

Publications

duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K "CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data." BMC Bioinformatics. 2016 Sep 13;17(1):363. https://doi.org/10.1186/s12859-016-1175-6
PMID: 27620863
PMCID: PMC5020541


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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