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  1. IGB
  2. IGBF-3448

Report edgeR and DESeq2 temperature-only DE genes from SL4 and SL5

        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:

          • Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
          • Do the same for SL4 annotations
          • Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
          • Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
          • Migrate volcano plot code to Common.R and show padj cutoff on the y axis
          • Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results

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              Task - A task that needs to be done. IGBF-3455 Visualize log fold-changes and p values to compare edgeR and DESeq2 results

              • 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-3446 [ 22548 ]
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 DE genes Compare edgeR to DESeq2 DE genes using SL4 and SL5 gene counts
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 DE genes using SL4 and SL5 gene counts Compare edgeR to DESeq2 temp-only DE genes using SL4 and SL5 gene counts
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 temp-only DE genes using SL4 and SL5 gene counts Compare edgeR to DESeq2 temp-only DE genes from SL4 and SL5
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 temp-only DE genes from SL4 and SL5 Compare and sanity-check edgeR and DESeq2 temperature-only DE genes from SL4 and SL5
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2 2023 Sep 17 [ 178 ] Fall 1 - Sep 5 [ 82 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 - Sep 5 [ 82 ] Fall 1 - Sep 5, Fall 2 2023 Sep 17 [ 82, 178 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                * Visualize log fold-changes and p values to compare edgeR and DESeq2 results
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                * Visualize log fold-changes and p values to compare edgeR and DESeq2 results                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                ann.loraine Ann Loraine made changes -
                Summary Compare and sanity-check edgeR and DESeq2 temperature-only DE genes from SL4 and SL5 Report edgeR and DESeq2 temperature-only DE genes from SL4 and SL5
                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 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3455 [ IGBF-3455 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                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 -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: