Uploaded image for project: 'IGB'
  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:
          None

          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.

            Attachments

              Issue Links

              blocks

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

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                bbendick Brandon Bendickson created issue -
                bbendick Brandon Bendickson made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                bbendick Brandon Bendickson made changes -
                Link This issue blocks IGBF-4230 [ IGBF-4230 ]
                bbendick Brandon Bendickson made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                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.

                Show
                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.
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

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

                Show
                bbendick Brandon Bendickson added a comment - Results found here: https://docs.google.com/spreadsheets/d/1V8bU1c1SkKg0J3pA5GHpi6NrJzf9fEta3hsWhGMBUag/edit?gid=1077548262#gid=1077548262
                bbendick Brandon Bendickson made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                bbendick Brandon Bendickson made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                bbendick Brandon Bendickson made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                bbendick Brandon Bendickson made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                bbendick Brandon Bendickson made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                bbendick Brandon Bendickson made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                bbendick Brandon Bendickson made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                bbendick Brandon Bendickson made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                bbendick Brandon Bendickson made changes -
                Resolution Done [ 10000 ]
                Status Closed [ 6 ] To-Do [ 10305 ]
                bbendick Brandon Bendickson made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                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

                Show
                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
                nfreese Nowlan Freese made changes -
                Sprint Summer 1 [ 218 ] Summer 1, Summer 2 [ 218, 219 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

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

                Show
                bbendick Brandon Bendickson added a comment - results found here: https://docs.google.com/spreadsheets/d/1tVyGO__YO_BVGnzHv0WnAq1JRuq342C3VIJliRmkwi4/edit?gid=262759742#gid=262759742
                bbendick Brandon Bendickson made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                bbendick Brandon Bendickson made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                bbendick Brandon Bendickson made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                bbendick Brandon Bendickson made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                bbendick Brandon Bendickson made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                bbendick Brandon Bendickson made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                bbendick Brandon Bendickson made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                bbendick Brandon Bendickson made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    bbendick Brandon Bendickson
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: