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sincell

sincell

sincell is an R tool for the assessment of cell-state hierarchies in single-cell RNA-seq (scRNA-seq) datasets. The package includes functions to compute cell-state hierarchies, statistics, accounts for random variations in the data, functional association tests, and graphics.

Topic

Transcriptomics; RNA-seq; RNA; Taxonomy

Details

  • Operation: RNA-Seq analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v>=2
  • Cost: Free
  • Version name: 1.18.0
  • Maturity: Stable
  • Credit: The European Unions Seventh Framework Programme FP7-2007-2013, the Swiss National Science Foundation.
  • Contact: Miguel Julia migueljuliamolina _at_ gmail.com, Antonio Rausell antonio.rausell _at_ isb-sib.ch
  • Collection: Bioconductor

Publications

Juliá M, Telenti A, Rausell A "Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq." Bioinformatics 2015; 31(20):3380-2 https://doi.org/10.1093/bioinformatics/btv368
PMID: 26099264
PMCID: PMC4595899


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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