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  1. IGB
  2. IGBF-4178

Vizualize the overall summary for EBSeq time course

        Details

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

          Description

          GOAL: To harness the EBSEQ-HMM run we did last fall and make some sort of easier way to summarize the overall trends of that data.

          I.,. How many gene in Heinz go up-up ? Up-down, etc.
          Repeat for each variety.

          Venn diagrams perhaps.........

          The data for this is here:
          https://drive.google.com/drive/folders/1Y03d2NFfXUvVa3_1_pt-WdwdvEDcLG63?usp=drive_link

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              Activity

              Ascending order - Click to sort in descending order
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              robofjoy Robert Reid added a comment -

              Step 1: Make files of each group. This is for Kelsey to handle the data easier.

              Heinz 25C UP-UP
              Heinz 37X Up-Up
              .
              .
              .Etc

              Show
              robofjoy Robert Reid added a comment - Step 1: Make files of each group. This is for Kelsey to handle the data easier. Heinz 25C UP-UP Heinz 37X Up-Up . . .Etc
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              robofjoy Robert Reid added a comment -

              2nd Step:

              ERrun EBSeqHMM and ensure it works fine.

              EbSeqHMM is not current with Bioconductor so we must use a previous verision of BioConductor (version 3.19) (Version 3.20 will not work)
              So my previous QMD file no longer works.

              Found 2 errors. Need to fix those first.

              Show
              robofjoy Robert Reid added a comment - 2nd Step: ERrun EBSeqHMM and ensure it works fine. EbSeqHMM is not current with Bioconductor so we must use a previous verision of BioConductor (version 3.19) (Version 3.20 will not work) So my previous QMD file no longer works. Found 2 errors. Need to fix those first.
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              robofjoy Robert Reid added a comment -

              Errors fixed!

              Results saved to GTTR Google Drive for Kelsey to have access.

              https://drive.google.com/drive/folders/1Y03d2NFfXUvVa3_1_pt-WdwdvEDcLG63?usp=drive_link

              Next phase. How to make these digestable. Redoing the overall summaries of the tables.

              Show
              robofjoy Robert Reid added a comment - Errors fixed! Results saved to GTTR Google Drive for Kelsey to have access. https://drive.google.com/drive/folders/1Y03d2NFfXUvVa3_1_pt-WdwdvEDcLG63?usp=drive_link Next phase. How to make these digestable. Redoing the overall summaries of the tables.
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              robofjoy Robert Reid added a comment -

              The idea is to have all points start at zero and show where how they go up or down across time.

              In the sheet in the comment above, a 2nd tab was added that summarizes the large table.

              Show
              robofjoy Robert Reid added a comment - The idea is to have all points start at zero and show where how they go up or down across time. In the sheet in the comment above, a 2nd tab was added that summarizes the large table.
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              bbendick Brandon Bendickson added a comment -

              Kelsey has accomplished this via her excel sheets.

              Show
              bbendick Brandon Bendickson added a comment - Kelsey has accomplished this via her excel sheets.

                People

                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: