2024 June updates

[sjspielman]

This issue tracks changes we should implement as noticed during June 2024's Intro scRNA-seq training.

[sjspielman]

Looks like the R4DS booked has moved, we should update links:
https://github.com/search?q=repo%3AAlexsLemonade%2Ftraining-modules%20r4ds&type=code

[sjspielman]

Too many spaces surrounding the comma at package , which:

training-modules/intro-to-R-tidyverse/03-intro_to_tidyverse.Rmd

Line 181 in 31bf431

_Note:_ If you are using a version of `R` prior to 4.1 (or looking at older code), pipe functionality was available through the `magrittr` package , which used a pipe that looked like this: `%>%`.

[jashapiro]

Apparently we may need to load the alevinQC package before running it.

training-modules/scRNA-seq/01-scRNA_quant_qc.Rmd

Lines 234 to 243 in 31bf431

	```{r alevinQC, eval = FALSE}
	# First, define path to alevin output:
	alevin_path <- file.path("data", "tabula-muris", "alevin-quant", "10X_P4_3_subset")
	# Produce a QC report of results found in the `alevin_path` directory
	alevinQC::alevinQCReport(alevin_path,
	sampleId = "10X_P4_3_subset",
	outputFile = "10X_P4_3_subset-qc_report.html",
	outputDir = "qc-reports")
	```

[sjspielman]

Just a thought as we make plots, should we use theme_set(theme_bw()) at the top of notebooks that make many plots?

[jaclyn-taroni]

Update this link to OSCA to use a current version of Bioconductor (3.19 at the moment):

training-modules/scRNA-seq/05-clustering_markers_scRNA.Rmd

Line 190 in 31bf431

For more detailed information about the methods presented here, including some ways to assess the "quality" of the clustering, I encourage you to explore at the relevant chapter of the [Orchestrating Single-Cell Analysis book](https://bioconductor.org/books/3.16/OSCA.basic/clustering.html#clustering-graph).

[jashapiro]

Update this link to OSCA to use a current version of Bioconductor (3.19 at the moment):

training-modules/scRNA-seq/05-clustering_markers_scRNA.Rmd

Line 190 in 31bf431

For more detailed information about the methods presented here, including some ways to assess the "quality" of the clustering, I encourage you to explore at the relevant chapter of the [Orchestrating Single-Cell Analysis book](https://bioconductor.org/books/3.16/OSCA.basic/clustering.html#clustering-graph).

All links to OSCA?

[sjspielman]

Cell type slides: We link review from 2021 about automated annotation tools, but 2021 is ages ago in single-cell time. Are there more recent papers we can reference here?