Changes between Version 25 and Version 26 of SOPs/go_annotation


Ignore:
Timestamp:
09/29/20 15:30:14 (4 years ago)
Author:
ibarrasa
Comment:

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  • SOPs/go_annotation

    v25 v26  
    3333     * 4. 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 ]]
    3434     * 5. Select your uploaded ranked list and click the run button. 
    35    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. You will need java 11. For Whitehead users: switch to java 11 with this command "ml java/10" (after this if you run "java --version" you will get "openjdk 11.0.8 2020-07-14")
     35   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.
    3636{{{
    37 gsea4cli GSEAPreranked -gmx ftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v7.2.symbols.gmt -norm meandiv -nperm 1000 -rnk myFile.rnk -scoring_scheme weighted -rpt_label my_analysis -create_svgs false -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 15 -zip_report false -out ./output
     37gsea-cli.sh GSEAPreranked -gmx ftp.broadinstitute.org://pub/gsea/gene_sets/h.all.v7.2.symbols.gmt -norm meandiv -nperm 1000 -rnk myFile.rnk -scoring_scheme weighted -rpt_label my_analysis -create_svgs false -make_sets true -plot_top_x 20 -rnd_seed timestamp -set_max 500 -set_min 15 -zip_report false -out ./output
    3838}}}
    39      * Notice that in our system ''gseacli'' points to ''gsea-cli.sh''. If you download your own version of GSEA you will have to run gsea-cli.sh   
     39   
    4040
    4141   ==== Traditional GSEA ====
    … …  
    4646
    4747
    48    ==== Fast gene set enrichment analysis (fgsea) ====
    49 [http://bioconductor.org/packages/release/bioc/html/fgsea.html |  fgsea]
    50 
    5148   ==== Single-sample GSEA (ssGSEA) ====
    5249  An extension of GSEA that can be used to determine enrichment of gene sets in individual samples.
     50
    5351
    5452More information
    5553
    5654* [[http://software.broadinstitute.org/webservices/gpModuleRepository/download/prod/module/?file=/ssGSEAProjection/broad.mit.edu:cancer.software.genepattern.module.analysis/00270/7.6/ssGSEAProjection.zip | Broad's ssGSEA from GenePattern R/jar scripts]]
     55
     56   ==== Fast gene set enrichment analysis (fgsea) ====
     57[[http://bioconductor.org/packages/release/bioc/html/fgsea.html | fgsea]] is an R-package for fast preranked GSEA. This package allows to quickly and accurately calculate arbitrarily low GSEA P-values for a collection of gene sets. You may want to try fgsea if the Broad GSEA takes too long to run.
    5758
    5859=== BiNGO ===