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  1. IGB
  2. IGBF-3355

Create Markdown consolidating DESeq treatment vs control analysis

        Details

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

          Description

          For this task, create a new Markdown named FindControlVsStressDEGenes-DESeq.Rmd

          The goal of this new Markdown is to compare treatment versus control samples for each genotype and each treatment duration.

          The Markdown will mirror FindControlVsStressDEGenes-edgeR.Rmd, saved in the same location of the repository.

          Both files will reside in the same folder. Also, both will output results files with the same format. The goal of doing this is to compare the DE genes found by each library.

          Also, the DeSeq Markdown will include volcano plots to summarize results.

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3372 Reorganize and prune muday bitbucket repo

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3356 Revise edgeR differential expression code to output results tables

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3339 Run relabeled 72-F3H-PollenTube data with Deseq analysis

              • Major - Major loss of function.
              • Closed

                Activity

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                aloraine Ann Loraine created issue -
                aloraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3277 [ 22158 ]
                aloraine Ann Loraine made changes -
                Link This issue relates to IGBF-3339 [ IGBF-3339 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ]
                aloraine Ann Loraine made changes -
                Link This issue relates to IGBF-3356 [ IGBF-3356 ]
                aloraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29 [ 171 ] Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis (Inactive) made changes -
                Comment [ Figured out formatting and functions. Now working on writing results correctly! ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ] Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis (Inactive) made changes -
                Link This issue blocks IGBF-3372 [ IGBF-3372 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Comment [ Cosmetic changes:
                * Square the plots
                * Create axis range (there is an outlier we are trying to remove in OE3 75 min plot that goes to 22 but has no p-value)
                * Change color from orange to red ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Attachment Muday-144-Combined-Volcano-Plots.pdf [ 17914 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Attachment Muday-144-Combined-Volcano-Plots.pdf [ 17914 ]
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                aloraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26 [ 171, 172, 173 ] Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 4 2023 June 26, Summer 5 2023 July 10 [ 171, 172, 173, 174 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ]
                aloraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                aloraine Ann Loraine made changes -
                Status Post-merge Testing In Progress [ 10003 ] To-Do [ 10305 ]
                aloraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
                aloraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                aloraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                aloraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                aloraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                aloraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                aloraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                aloraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Mdavis4290 Molly Davis (Inactive) made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                aloraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                aloraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                aloraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis (Inactive)
                    Reporter:
                    aloraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: