diff --git a/20-r-rstudio.md b/20-r-rstudio.md index 16ab3b575..a79afbf6e 100644 --- a/20-r-rstudio.md +++ b/20-r-rstudio.md @@ -582,7 +582,7 @@ sessionInfo() ``` ```{.output} -R version 4.3.1 (2023-06-16) +R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS @@ -603,7 +603,7 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): -[1] BiocManager_1.30.22 compiler_4.3.1 tools_4.3.1 +[1] BiocManager_1.30.22 compiler_4.3.2 tools_4.3.2 [4] yaml_2.3.7 highr_0.10 knitr_1.45 [7] xfun_0.41 renv_1.0.3 evaluate_0.23 ``` diff --git a/config.yaml b/config.yaml deleted file mode 100644 index 13c9b4377..000000000 --- a/config.yaml +++ /dev/null @@ -1,85 +0,0 @@ -#------------------------------------------------------------ -# Values for this lesson. -#------------------------------------------------------------ - -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -carpentry: 'incubator' - -# Overall title for pages. -title: 'Introduction to data analysis with R and Bioconductor' - -# Date the lesson was created (YYYY-MM-DD, this is empty by default) -created: '2020-09-14' - -# Comma-separated list of keywords for the lesson -keywords: 'software, data, lesson, The Carpentries' - -# Life cycle stage of the lesson -# possible values: pre-alpha, alpha, beta, stable -life_cycle: 'stable' - -# License of the lesson -license: 'CC-BY 4.0' - -# Link to the source repository for this lesson -source: 'https://github.com/carpentries-incubator/bioc-intro' - -# Default branch of your lesson -branch: 'main' - -# Who to contact if there are any issues -contact: 'laurent.gatto@uclouvain.be' - -# Navigation ------------------------------------------------ -# -# Use the following menu items to specify the order of -# individual pages in each dropdown section. Leave blank to -# include all pages in the folder. -# -# Example ------------- -# -# episodes: -# - introduction.md -# - first-steps.md -# -# learners: -# - setup.md -# -# instructors: -# - instructor-notes.md -# -# profiles: -# - one-learner.md -# - another-learner.md - -# Order of episodes in your lesson -episodes: -- 10-data-organisation.Rmd -- 20-r-rstudio.Rmd -- 23-starting-with-r.Rmd -- 25-starting-with-data.Rmd -- 30-dplyr.Rmd -- 40-visualization.Rmd -- 60-next-steps.Rmd - -# Information for Learners -learners: - -# Information for Instructors -instructors: - -# Learner Profiles -profiles: - -# Customisation --------------------------------------------- -# -# This space below is where custom yaml items (e.g. pinning -# sandpaper and varnish versions) should live - - -url: 'https://carpentries-incubator.github.io/bioc-intro' diff --git a/fig/40-visualization-rendered-boxplot-color-time-1.png b/fig/40-visualization-rendered-boxplot-color-time-1.png index d4222ba17..e33631beb 100644 Binary files a/fig/40-visualization-rendered-boxplot-color-time-1.png and b/fig/40-visualization-rendered-boxplot-color-time-1.png differ diff --git a/fig/40-visualization-rendered-boxplot-color-time-2.png b/fig/40-visualization-rendered-boxplot-color-time-2.png index 83dc3cd18..03d20ffae 100644 Binary files a/fig/40-visualization-rendered-boxplot-color-time-2.png and b/fig/40-visualization-rendered-boxplot-color-time-2.png differ diff --git a/fig/40-visualization-rendered-boxplot-with-points-1.png b/fig/40-visualization-rendered-boxplot-with-points-1.png index 9ed382798..225892b40 100644 Binary files a/fig/40-visualization-rendered-boxplot-with-points-1.png and b/fig/40-visualization-rendered-boxplot-with-points-1.png differ diff --git a/fig/40-visualization-rendered-boxplot-with-points2-1.png b/fig/40-visualization-rendered-boxplot-with-points2-1.png index 0e9a639af..3b6a8618b 100644 Binary files a/fig/40-visualization-rendered-boxplot-with-points2-1.png and b/fig/40-visualization-rendered-boxplot-with-points2-1.png differ diff --git a/fig/40-visualization-rendered-boxplot-xaxis-rotated-1.png b/fig/40-visualization-rendered-boxplot-xaxis-rotated-1.png index e1042bd05..ab14c457d 100644 Binary files a/fig/40-visualization-rendered-boxplot-xaxis-rotated-1.png and b/fig/40-visualization-rendered-boxplot-xaxis-rotated-1.png differ diff --git a/fig/40-visualization-rendered-color-by-gene_biotype3-1.png b/fig/40-visualization-rendered-color-by-gene_biotype3-1.png index 01135f9a3..18bb8ce96 100644 Binary files a/fig/40-visualization-rendered-color-by-gene_biotype3-1.png and b/fig/40-visualization-rendered-color-by-gene_biotype3-1.png differ diff --git a/fig/40-visualization-rendered-plotmethod-1.png b/fig/40-visualization-rendered-plotmethod-1.png index f766b1db7..852e96f99 100644 Binary files a/fig/40-visualization-rendered-plotmethod-1.png and b/fig/40-visualization-rendered-plotmethod-1.png differ diff --git a/md5sum.txt b/md5sum.txt index 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