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  1. IGB
  2. IGBF-4159

ComplexUpsetR from big table KelseyRun-unpol

        Details

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

          Description

          Once we have big tables of our expressed genes (IGBF-4154), let's make complexUpsetR plots in various ways.

          Big one with all !

          4 X variety ones.

          3hrX8hrs
          25c x 37c

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              is blocked by

              Task - A task that needs to be done. IGBF-4154 Kelsey run Get gene differentiation btw 25C and 37C-Unpollinated pistil study

              • Major - Major loss of function.
              • Closed

                Activity

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                robofjoy Robert Reid created issue -
                robofjoy Robert Reid made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                robofjoy Robert Reid made changes -
                Link This issue is blocked by IGBF-4154 [ IGBF-4154 ]
                bbendick Brandon Bendickson made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                bbendick Brandon Bendickson added a comment -

                Note for Brandon:
                Make ven diagram of all genes in all 4 varieties at 3hr and 8hr. We want to visualize the "core" genes that are present in all varieties at 3hr and 8hr to see the overlap.

                Show
                bbendick Brandon Bendickson added a comment - Note for Brandon: Make ven diagram of all genes in all 4 varieties at 3hr and 8hr. We want to visualize the "core" genes that are present in all varieties at 3hr and 8hr to see the overlap.
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                robofjoy Robert Reid added a comment -


                And then after repeat this again but leave Heinz out. Look at all genes that express in the 3 TMN varieties (but not in Heinz).

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                robofjoy Robert Reid added a comment - And then after repeat this again but leave Heinz out. Look at all genes that express in the 3 TMN varieties (but not in Heinz).
                robofjoy Robert Reid made changes -
                Attachment input4complexUpset.tsv [ 18665 ]
                robofjoy Robert Reid made changes -
                Attachment ComplexUpsetR_example.R [ 18666 ]
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                robofjoy Robert Reid added a comment -

                input4complexUpset.tsv

                This is the example dataset to test the bar graphs.

                ComplexUpsetR_example.R

                And example R script. Just need to point at correct file location.

                Show
                robofjoy Robert Reid added a comment - input4complexUpset.tsv This is the example dataset to test the bar graphs. ComplexUpsetR_example.R And example R script. Just need to point at correct file location.
                ann.loraine Ann Loraine made changes -
                Sprint Spring 5 [ 214 ] Spring 5, Spring 6 [ 214, 215 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                bbendick Brandon Bendickson made changes -
                Status To-Do [ 10305 ] 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:
                    robofjoy Robert Reid
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: