source commit: 093fd0a

01-helpers.R

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+r_version_string <- function() {
+  paste0(R.version$major, ".", R.version$minor)
+}
+
+r_version_string.patch_x <- function() {
+  gsub(".$", "x", r_version_string())
+}

01-setup.md

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+---
+source: Rmd
+title: Introduction and setup
+teaching: XX
+exercises: XX
+---
+
+
+
+::::::::::::::::::::::::::::::::::::::: objectives
+
+- Ensure that participants are using the correct version of R to reproduce exactly the contents of this lesson.
+- Download the example files for this lesson.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+:::::::::::::::::::::::::::::::::::::::: questions
+
+- Am I using the correct version of R for this lesson?
+- Why does my version of R matter?
+- How do I obtain the files that are used in this lesson?
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+## Version of R
+
+This lesson was developed and tested with R version 4.4.1 (2024-06-14).
+
+Take a moment to launch RStudio and verify that you are using R version 4.4.x, with `x` being any patch version, e.g. 4.4.1.
+
+
+``` r
+R.version.string
+```
+
+``` output
+[1] "R version 4.4.1 (2024-06-14)"
+```
+
+This is important because Bioconductor uses the version of R running in the current session to determine the version of Bioconductor packages that can be installed in the R library associated with the current R session.
+Using a different version of R while following this lesson may lead to unexpected results.
+
+## Download files
+
+Several episodes in this lesson rely on example files that participants need to download.
+
+Run the code below programmatically create a folder called `data` in the current working directory, and download the lesson files in that folder.
+
+
+``` r
+dir.create("data", showWarnings = FALSE)
+download.file(
+    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/TrimmomaticAdapters/TruSeq3-PE-2.fa", 
+    destfile = "data/TruSeq3-PE-2.fa"
+)
+download.file(
+    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/ActbGtf/actb.gtf", 
+    destfile = "data/actb.gtf"
+)
+download.file(
+    url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/master/data/ActbOrf/actb_orfs.fasta", 
+    destfile = "data/actb_orfs.fasta"
+)
+download.file(
+  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/counts.csv",
+  destfile = "data/counts.csv"
+)
+download.file(
+  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/gene_metadata.csv",
+  destfile = "data/gene_metadata.csv"
+)
+download.file(
+  url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/sample_metadata.csv",
+  destfile = "data/sample_metadata.csv"
+)
+```
+
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## Note
+
+Ideally, participants might want to create a new [RStudio project][external-rstudio-project] and download the lesson files in a sub-directory of that project.
+
+Using an RStudio project sets the working directory to the root directory of that project.
+As a consequence, code is executed relative to that root directory, often avoiding the need for using absolute file paths to import/export data from/to files.
+
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+[external-rstudio-project]: https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects
+
+
+:::::::::::::::::::::::::::::::::::::::: keypoints
+
+- Participants will only be able to install the version of Bioconductor packages described in this lesson and reproduce their exact outputs if they use the correct version of R.
+- The files used in this lesson should be downloaded in a local path that is easily accessible from an R session.
+
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
+