Update intro R materials

[sjspielman]

Closes #860
Closes #909
Stacked on #915; I'm opening this as a Draft until its target is master (no huge rush on this PR)

This PR takes care of remaining intro R materials to update.

1. For Remove penguins package #909, remove palmerpenguins from renv and update notebook language/variables accordingly. Let me know any wording feedback!
2. To close out 2025 August updates: Intro to scRNA-seq #860:
   • New line for notebook rendering: 2025 August updates: Intro to scRNA-seq #860 (comment)
   • I updated the 03 notebook to use :: all around in the code. We introduce mutate & filter already in the 02 notebook, so they will have already a bit of dplyr before getting here: 2025 August updates: Intro to scRNA-seq #860 (comment)
   • I added the ggplot2 book and removed socviz which is pretty old at this point: 2025 August updates: Intro to scRNA-seq #860 (comment)
   • Summarize updates: 2025 August updates: Intro to scRNA-seq #860 (comment)

Note:

• I opened a separate issue for this comment in the exercise repo: 2025 August updates: Intro to scRNA-seq #860 (comment)
• I didn't change any file.path() syntax

[sjspielman]

Noting I'm going to keep this as a Draft at least until #926 goes in due to conflicts, maybe a bit longer due to priorities.