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  1. IGB
  2. IGBF-3459

Re-org and document flavonoid git repository

    Details

    • Type: Task
    • Status: To-Do (View Workflow)
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      Add documentation to the repo explaining what each file is.

        Attachments

          Activity

          Show
          ann.loraine Ann Loraine added a comment - Added "README" to https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/72_F3H_PollenTube/results/
          Hide
          ann.loraine Ann Loraine added a comment -

          There is redundancy between functions in files Common.R and StyleFunctions.R.
          Also, it would be good to split out the statistical library-using functions from Common.R to a different R script, reducing requirement for installing / loading libraries among potential users who just want to interact with the results and not re-run library methods.
          Am working on re-org-ing the files. Also, am working on making sure the older .Rmd's can run.

          Show
          ann.loraine Ann Loraine added a comment - There is redundancy between functions in files Common.R and StyleFunctions.R. Also, it would be good to split out the statistical library-using functions from Common.R to a different R script, reducing requirement for installing / loading libraries among potential users who just want to interact with the results and not re-run library methods. Am working on re-org-ing the files. Also, am working on making sure the older .Rmd's can run.
          Hide
          ann.loraine Ann Loraine added a comment -

          Instead of pushing directly to main branch on team repository, using branch on my fork: https://bitbucket.org/aloraine/flavonoid-rnaseq/src/main/

          Link to branch: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3459

          Show
          ann.loraine Ann Loraine added a comment - Instead of pushing directly to main branch on team repository, using branch on my fork: https://bitbucket.org/aloraine/flavonoid-rnaseq/src/main/ Link to branch: https://bitbucket.org/aloraine/flavonoid-rnaseq/branch/IGBF-3459
          Hide
          Mdavis4290 Molly Davis added a comment - - edited

          Notes about repo:

          • Muday-144_genotype.R can be deleted as it was a script draft of the temp and genotype analysis
          • Possibly move ARE-120min-analysis folder out of this repo for clarity for readers
          • Change 72_F3H_PollenTube folder name
          • Possibly rename FindControlVsStressDEGenes-[assembly]-[method].Rmd files due to the lab not knowing where the volcano plots are in the repo
          • There are two igb_images folders in the repo. One in the main flavonoid-rnaseq area and the other in 72_F3H_PollenTube
          • Do we need obsolete folder in 72_F3H_PollenTube
          Show
          Mdavis4290 Molly Davis added a comment - - edited Notes about repo : Muday-144_genotype.R can be deleted as it was a script draft of the temp and genotype analysis Possibly move ARE-120min-analysis folder out of this repo for clarity for readers Change 72_F3H_PollenTube folder name Possibly rename FindControlVsStressDEGenes- [assembly] - [method] .Rmd files due to the lab not knowing where the volcano plots are in the repo There are two igb_images folders in the repo. One in the main flavonoid-rnaseq area and the other in 72_F3H_PollenTube Do we need obsolete folder in 72_F3H_PollenTube
          Hide
          ann.loraine Ann Loraine added a comment -

          Merged branch into main.

          Show
          ann.loraine Ann Loraine added a comment - Merged branch into main.
          Hide
          ann.loraine Ann Loraine added a comment -

          For the reorg, I would like to keep the 120 minutes time point data in the repository. I want to keep all the history for that folder / data set intact and available for future work.

          Show
          ann.loraine Ann Loraine added a comment - For the reorg, I would like to keep the 120 minutes time point data in the repository. I want to keep all the history for that folder / data set intact and available for future work.

            People

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

              • Created:
                Updated: