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splatter

splatter

splatter is a tool for simulation of single-cell RNA-seq (scRNA-seq) data. The algorithm can estimate the parameters from real data sets. The splatter tool also combines an interface for several simulations methods, such as Splat which is based on a gamma-Poisson distribution.

Topic

Gene expression; RNA-seq; Sequencing; Transcriptomics

Details

  • Operation: Modelling and simulation; Comparison
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.10.0
  • Maturity: Stable
  • Credit: Australian Government Research Training Program (RTP) Scholarship, National Health, Medical Research Council Career Development Fellowship, the Victorian Governments Operational Infrastructure Support Program.
  • Contact: Luke Zappia luke.zappia _at_ mcri.edu.au
  • Collection: Bioconductor

Publications

Zappia L, Phipson B, Oshlack A "Splatter: simulation of single-cell RNA sequencing data." Genome Biol. 2017; 18(1):174 https://doi.org/10.1186/s13059-017-1305-0
PMID: 28899397
PMCID: PMC5596896


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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