Gaggle

1. Start an optional Gaggle Boss
2. Annotation
   • Thaps Protein ID, EC numbers, and Annotations
   • JGI links for Thaps protein IDs in filtered set
3. Proteomics
   • Proteomics data in the dmv
4. Sequence
   • Thalassiosira transcript sequences (DNA and amino acid)
5. Analysis Tools
   • MeV MultiExperiment Viewer microarray data analysis tool.
     • For general information on MeV see the TM4 website.
   • 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 way of visualizing data plotted against coordinates on the genome. Tiling arrays and ChIP-chip data are a couple use cases.