Changes between Version 22 and Version 23 of SOPs/go_annotation


Ignore:
Timestamp:
09/29/20 13:24:49 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/go_annotation

    v22 v23  
    4646  An extension of GSEA that can be used to determine enrichment of gene sets in individual samples.
    4747
    48   [[http://rowley.mit.edu/caw_web/ssGSEAProjection/ssGSEA_caw_BIG_120314.pptx | ssGSEA Presentation from MIT BMC ]]
     48More information
    4949
    50 [[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
     50* [[http://rowley.mit.edu/caw_web/ssGSEAProjection/ssGSEA_caw_BIG_120314.pptx | ssGSEA Presentation from MIT BMC ]]
    5151
    52 [[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.
     52* [[https://www.gsea-msigdb.org/gsea/login.jsp|Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.]]
    5353
    54 [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page | GSEA and MSigDB documentation]]
     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.
    5555
    56 [[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Using_RNA-seq_Datasets_with_GSEA | Guidelines for using RNA-seq datasets with GSEA]]
    57   [[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]]
     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]]
    5858
    59   * NOTE: GSEA should be run on the 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)]]
     59* [[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)]]
    6062
    6163=== BiNGO ===