Manuscript Submission Checklist

When working on a manuscript to submit to a journal, these tasks should be completed prior to submission. Chat with Evan if your circumstances necessitate adaptation.

Manuscript

• [ ] Written and styled according to Journal Guidelines
• [ ] Shared with Pod for feedback w/ accompanying code (see below)
• [ ] Feedback from Pod incorporated
• [ ] Shared with collaborators w/ accompanying code
• [ ] Submitted to biorxiv or other preprint server
• [ ] Submit to Journal

Code to Accompany Manuscript

• [ ] All Code is hosted on GitHub
  • [ ] R Markdown file that follows the flow of your manuscript, including:
    • [ ] Starting with raw data retrieval
    • [ ] Cleaning/pre-processing data
    • [ ] Analyzing data
    • [ ] Figure creation
    • [ ] sessionInfo() code block
    • [ ] Descriptions throughout the document
  • [ ] R Markdown PDF/HTML
    • Timeless instance of your work
  • [ ] R folder
    • [ ] Separate file for any functions you created to simplify your RMarkdown file or that other users should use to implement your findings in their own work
    • [ ] Each function should have a roxygen description
    • [ ] Functions that readers should use should include an example in the roxygen description
  • [ ] README file
    • [ ] Description of how to use the files in the repository
    • [ ] Point to the R Markdown file that contains manuscript analyses and figures
  • [ ] Specifically direct the user to functions that they should use in their own work (or to packages that may contain this info)
  • [ ] DESCRIPTION file
    • [ ] See requirements for R packages (https://r-pkgs.org/description.html)
    • [ ] Includes: package (analysis) name, title, authors, imports (list of all required packages), R version used, etc
  • [ ] Data Folder (if data is not hosted elsewhere and retrieved in rMarkdown file)
    • [ ] Contains all data for analysis
• [ ] Data has been submitted to an appropriate database (ex: Sequence Read Archive)
• [ ] Repository provided to Pod for Review, including:
  1. Fork the repository to your own GitHub
  2. Replicate the R Markdown on personal machine
     • [ ] Should match the knit PDF R markdown file provided in the repository
     • [ ] Can you access all the data used in the analysis?
     • [ ] If differences exist, ensure it is not a version issue or a run time environment difference
     • [ ] Only move to steps 2 and 3 when this step is complete; meet as soon as possible with the developer if problems arise
  3. Is the code clearly commented and easily readable?
     • [ ] R Markdown is clear and follows the flow of the manuscript
     • [ ] R folder functions all have clear roxygen comments
  4. Any other vital changes that may be needed
  5. Record Feedback as “Issues” and/or provide pull request for edits
• [ ] Code updated based on Reviewer Feedback
• [ ] Once finalized, ensure that a forked version is available on wejlab page (Evan, Jessica, or Aubrey can do this)