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DEBrowser

DEBrowser

DEBrowser is an R Shiny app for step-wise visualizing expression data from RNA-seq. The debrowser package has methods to plot various types of graphs, such as scatter, box, bar, heatmaps, MA, and volcano.

Topic

Gene expression

Details

  • Operation: Differential gene expression analysis
  • Software interface: Command-line user interface; Webuser interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GPL-3.0
  • Cost: Free
  • Version name: 1.14.0
  • Maturity: Stable
  • Credit: the National Human Genome Research Institute NHGRI, he National Center for Advancing Translational Sciences.
  • Contact: Alper Kucukural alper.kucukural _at_ umassmed.edu
  • Collection: BioConductor

Publications

Kucukural A, Yukselen O, Ozata DM, Moore MJ, Garber M "DEBrowser: interactive differential expression analysis and visualization tool for count data." BMC Genomics. 2019 Jan 5;20(1):6. https://doi.org/10.1186/s12864-018-5362-x
PMID: 30611200
PMCID: PMC6321710


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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