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  1. IGB
  2. IGBF-3356

Revise edgeR differential expression code to output results tables

        Details

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

          Description

          The current version does not write out DE gene results. Also, the name of the file is not specific enough.

          For this task:

          • Change name of FindDifferentiallyExpressedGenes.Rmd (and its knitted .PDF) to: FindControlVsStressDEGenes-edgeR.Rmd
          • Write out a consolidated .txt file reporting differential expression results

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3342 Create scaled counts file for Muday analysis

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3355 Create Markdown consolidating DESeq treatment vs control analysis

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3277 [ 22158 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3355 [ IGBF-3355 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                ann.loraine Ann Loraine made changes -
                Description The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and knitted .PDF) to:
                ann.loraine Ann Loraine made changes -
                Description The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and knitted .PDF) to:                 		The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and its knitted .PDF) to: FindControlVsStressDEGenes-edgeR.Rmd
                * Write out a consolidated .txt file reporting differential expression results
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29 [ 171 ] Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3342 [ IGBF-3342 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: