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SGSeq

SGSeq

SGSeq is a tool to predict and quantify splice events in RNA-seq datasets. The SGSeq algorithm predicts splice junctions and exons by mapping reads to a reference genome.

Topic

RNA-Seq; RNA splicing

Details

  • Operation: Sequence visualisation
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 1.20.0
  • Maturity: Stable
  • Credit: Genentech Inc.
  • Contact: Leonard Goldstein goldstel _at_ gene.com
  • Collection: Bioconductor

Publications

Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R "Prediction and Quantification of Splice Events from RNA-Seq Data." PLoS ONE 2016; 11(5):e0156132 https://doi.org/10.1371/journal.pone.0156132
PMID: 27218464
PMCID: PMC4878813


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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