Gaggle Components
Geese
Data Standards
Boss

Haloarcula marismortui (2007-04)

Gaggle

  1. Optionally start a Gaggle Boss
  2. Annotations
  3. Cytoscape Networks
    • network (edges from Rich Bonneau).
  4. Microarray Data
    • Blank DMV. Use the Data Matrix Viewer to load your own microarray data.
      1. File|Load|Tab-Delimited file (Browse to the appropriate directory and load a file of this format.)
      2. For more information on using DMV go here.
  5. Analysis Tools
    • MeV MultiExperiment Viewer microarray data analysis tool.
    • R statistics package
      • If R and the Gaggle package are not installed, see these instructions.
      • Connect R to the Gaggle, as described in 'Startup'.
        • At the R prompt, type these commands (in R 2.4.x):
          
          library(gaggle)
          source("http://gaggle.systemsbiology.net/R/gaggleUtil.R")
          gaggleInit()
          
      • See the cribsheet for quick instructions on how to accomplish common tasks using R and the R goose.
    • Firegoose
      • If the Firegoose extension is not installed, see these instructions.
      • Start the Firefox browser.
      • Use the Paster Application to paste data into Firegoose.
    • Genome Browser
      • The genome browser is a tool for visualizing data plotted against coordinates on the genome. Tiling arrays and ChIP-chip data are a couple use cases.
    • BioTapestry

External Links

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