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Course materials for "MOLB 7950: Informatics and Statistics for Molecular Biology".

Create a new template project and manually install packages.

While renv is a nice idea and is helpful for local development, in practiceit doesn't seem robust enough on Posit Cloud.

If you wanted to try using renv, clone the direction and then runrenv::activate() andrenv::restore(), which will install projectpackages in a project-local library underrenv/.

If you add new libraries to your content, runrenv::snapshot(), followinstructions torenv::install() if needed, and then be sure to commit therenv.lock file.

You can also trying usingpak for installation by settingRENV_CONFIG_PAK_ENABLED = TRUE in the user's.Renviron file(usethis::edit_r_environ()) to use pak installation,which is a lot faster (issue).In practice, pak with renv seems a bit flaky.

Usequarto render orquarto preview locally to inspect content prior tocommit / push. A Github Action builds the site automatically unless you include[ci skip] in the commit message.

After a significant update (i.e., uploading a lot of class material), you shouldquarto render the entire site, and then commit & push the contents of the_freeze directory,which will enable rendering of only changed materials relative to that build.

Pages should be named based on the syllabus table, e.g.,class-01.qmd.

The qmd files you want rendered as slides go inslides/,exercises/,problem-sets/, andproblem-set-keys/

Each of these will be linked in the table on the front page.

If you want to suppress quarto rendering of a file, prefix the filename with an underscore like_class-01.qmd.

1. Edit the "Syllabus" sheet on theGoogleSheet.Contact Jay if you need access.
2. Rundata-raw/syllabus.R. You may be prompted to authenticate (onetime). The writes a newdata/syllabus.tsv file.
3. Re-render the page (quarto render index.qmd) and check formatting.
4. Commit and push to GitHub.

• Problem sets and keys live here:https://github.com/rnabioco/molb-7950-problem-sets

• Large data sets, mainly single-cell problem sets, live here (so we don't bloat this repo):https://github.com/rnabioco/molb-7950-data/

This work borrows from and modifies:https://github.com/mine-cetinkaya-rundel/quarto-sdss