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  1. IGB
  2. IGBF-4229

Run GAGE for all comparisons

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          Run gage on our tpm normalized counts table and get all desired comparisons. Make a large excel sheet that displays the resulting tables, focus on greater/lesser results. Use the results to make a cool upset plot of overlapping pathways.

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              Task - A task that needs to be done. IGBF-4230 Create Complex Upset plot of GAGE pathways

              • Major - Major loss of function.
              • Closed

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                bbendick Brandon Bendickson added a comment -

                results found here: https://docs.google.com/spreadsheets/d/1tVyGO__YO_BVGnzHv0WnAq1JRuq342C3VIJliRmkwi4/edit?gid=262759742#gid=262759742

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                bbendick Brandon Bendickson added a comment - results found here: https://docs.google.com/spreadsheets/d/1tVyGO__YO_BVGnzHv0WnAq1JRuq342C3VIJliRmkwi4/edit?gid=262759742#gid=262759742
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                bbendick Brandon Bendickson added a comment -

                Something is wrong! take a step back and try different plans of attack. Lets try GAGE with deseq data or with ranked test over KS

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                bbendick Brandon Bendickson added a comment - Something is wrong! take a step back and try different plans of attack. Lets try GAGE with deseq data or with ranked test over KS
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                bbendick Brandon Bendickson added a comment -

                Results found here: https://docs.google.com/spreadsheets/d/1V8bU1c1SkKg0J3pA5GHpi6NrJzf9fEta3hsWhGMBUag/edit?gid=1077548262#gid=1077548262

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                bbendick Brandon Bendickson added a comment - Results found here: https://docs.google.com/spreadsheets/d/1V8bU1c1SkKg0J3pA5GHpi6NrJzf9fEta3hsWhGMBUag/edit?gid=1077548262#gid=1077548262
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                bbendick Brandon Bendickson added a comment -

                Ran gage for all standard comparisons (same variety, different temp, 3hr and 8hr) using the KS test, moving on to making an upset plot.

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                bbendick Brandon Bendickson added a comment - Ran gage for all standard comparisons (same variety, different temp, 3hr and 8hr) using the KS test, moving on to making an upset plot.

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    bbendick Brandon Bendickson
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                    Dates

                    • Created:
                      Updated:
                      Resolved: