Changes between Version 23 and Version 24 of SOPs/go_annotation


Ignore:
Timestamp:
09/29/20 13:57:37 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/go_annotation

    v23 v24  
    1515
    1616GSEA can be run on about any operating system (so on your own computer or on a Whitehead Linux server like tak).
     17
     18==== Introductory information about GSEA ====
     19
     20* [[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
     21* [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|Explore the Molecular Signatures Database (MSigDB), ]]a collection of annotated gene sets for use with GSEA software.
     22* [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA and MSigDB documentation]]
     23* [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | Guidelines for using RNA-seq datasets with GSEA]]
    1724 
    1825   ==== GSEAPreranked: start with a list of genes and values ====
    … …  
    3340   ==== Unranked List ====
    3441 
    35 GSEA will rank the genes
     42Traditional GSEA
    3643
    3744  1.  Create necessary files in correct format for expression, phenotype and chip annotation ([[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | see GSEA wiki]])
    … …  
    4855More information
    4956
    50 * [[http://rowley.mit.edu/caw_web/ssGSEAProjection/ssGSEA_caw_BIG_120314.pptx | ssGSEA Presentation from MIT BMC ]]
    51 
    52 * [[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
    53 
    54 * [[https://www.gsea-msigdb.org/gsea/msigdb/index.jsp|Explore the Molecular Signatures Database (MSigDB), ]]a collection of annotated gene sets for use with GSEA software.
    55 
    56 * [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA and MSigDB documentation]]
    57 * [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | Guidelines for using RNA-seq datasets with GSEA]]
    58 
    5957* [[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]]
    60 
    61   * GSEA should be run on one's entire dataset, and not a subset of genes as this may bias the results. See [[https://groups.google.com/forum/#!searchin/gsea-help/subset%7Csort:date/gsea-help/INJ1RpLOBWk/1qwnsMOYAQAJ | GSEA pre-ranked questions (Google Groups)]]
    6258
    6359=== BiNGO ===