C2G2 07-08-2013 MUSC

Agenda
 * 1) Update on Lung Cancer Processing (Matt and Connor)
 * 2) Update on PDEF/Fli1 pathway analysis (GAGE and other tools) (Connor)
 * 3) Using the pathway analysis tools, common problem is lack of replicates.
 * 4) GAGE (generally applicable gene-set/pathway analysis) produces relevant heatmaps and venn diagrams that show significantly up and/or down regulated genesets and pathways
 * 5) GSVA
 * 6) SeqGSEA uses both DE and DS data also uses DeSeq as a differential expression pipeline, in addition also requires at least 3 replicates in order to work.
 * 7) gene names and fold change to Bob Wilson for pathway .txt
 * 8) Try a comparison of reactome
 * 9) Update on overall machine configuration/cluster health, etc (Paul and Matt)
 * 10) Update on cloud integration (Jeremy)
 * 11) demo and clean up
 * 12) Alligator file conversion (Matt)
 * 13) Upcoming schedules and travel (Paul and Andy)
 * 14) Schedule and goals for the rest of the summer (everyone)