Changes between Version 15 and Version 16 of SOPs/go_annotation


Ignore:
Timestamp:
09/28/20 11:52:33 (4 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/go_annotation

    v15 v16  
    2929     * 3. Select one of the gene sets from the "Gene sets database". We recommend starting with the Hallmarks set (h.all). You can find more information about the sets [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|here ]]
    3030     * 4. Select your uploaded ranked list and click the run button. 
    31    3. To run the same type of analysis on the command line, use a command like
     31   3. To run the same type of analysis on the command line, you can see the command the GUI used clicking the "Command" button and run that command in your Linux machine.
    3232{{{
    3333java -Xmx512m -cp /usr/lib/share/gsea2/gsea2-2.2.2.jar xtools.gsea.GseaPreranked -gmx gseaftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v5.2.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -rnk ./MY_COMPARISON.rnk -scoring_scheme weighted -rpt_label GSEA_out_v1 -chip gseaftp.broadinstitute.org://pub/gsea/annotations/GENE_SYMBOL.chip -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 2 -zip_report false -out GSEA_OUT.TEST_v1 -gui false