Changes between Version 19 and Version 20 of SOPs/go_annotation

Timestamp:

09/28/20 16:22:24 (4 years ago)

Author:

ibarrasa

Comment:

--

SOPs/go_annotation

@@ -31 +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. 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")
 {{{
-gsea-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
+gseacli 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
 }}}
+     * 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   
    ==== Unranked List ====
  
@@ -43 +44 @@
 
    ==== Fast gene set enrichment analysis (fgsea) ====
-[http://bioconductor.org/packages/release/bioc/html/fgsea.html/ fgsea]
+[http://bioconductor.org/packages/release/bioc/html/fgsea.html |  fgsea]
 
    ==== Single-sample GSEA (ssGSEA) ====