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EDASeq

EDASeq

EDASeq is an R tool for visualization of RNA-seq data. The EDASeq includes functions for within lane and between lane normalizations.

Topic

RNA-Seq; Sequence analysis

Details

  • Operation: Sequence visualisation; RNA-Seq analysis
  • Software interface: Command-line user interface
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic-2.0
  • Cost: Free
  • Version name: 2.20.0
  • Maturity: Mature
  • Credit: The National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), University of Padua.
  • Contact: Davide Risso risso.davide _at_ gmail.com
  • Collection: Bioconductor

Publications

Risso D, Schwartz K, Sherlock G, Dudoit S "GC-content normalization for RNA-Seq data." BMC Bioinformatics. 2011 Dec 17;12:480. https://doi.org/10.1186/1471-2105-12-480
PMID: 22177264
PMCID: PMC3315510


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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