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carpentries-incubator / bioc-rnaseq

Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
https://carpentries-incubator.github.io/bioc-rnaseq
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Reorg #42

Closed jdrnevich closed 1 year ago

jdrnevich commented 1 year ago

Major reorganization of episodes; collapsing some and moving others up

github-actions[bot] commented 1 year ago

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-42

The following changes were observed in the rendered markdown documents:

 02-intro-to-rnaseq.md => 01-intro-to-rnaseq.md     |   1 +
 01-introduction.md (gone)                          |  36 -------
 02-setup.md (new)                                  | 110 +++++++++++++++++++++
 05-import-annotate.md => 03-import-annotate.md     |   0
 03-setup.md (gone)                                 |  55 -----------
 06-exploratory-qc.md => 04-exploratory-qc.md       |  12 +--
 ...-expression.md => 05-differential-expression.md |   8 +-
 08-gene-set-analysis.md => 06-gene-set-analysis.md |   0
 09-next-steps.md => 07-next-steps.md               |   0
 04-experimental-design.md => 08-extra-design.md    |  20 ++--
 config.yaml                                        |  17 ++--
 ...exploratory-qc-rendered-unnamed-chunk-10-1.png} | Bin
 ...-exploratory-qc-rendered-unnamed-chunk-5-1.png} | Bin
 ...-exploratory-qc-rendered-unnamed-chunk-6-1.png} | Bin
 ...-exploratory-qc-rendered-unnamed-chunk-7-1.png} | Bin
 ...-exploratory-qc-rendered-unnamed-chunk-8-1.png} | Bin
 ...-exploratory-qc-rendered-unnamed-chunk-9-1.png} | Bin
 ...tial-expression-rendered-unnamed-chunk-6-1.png} | Bin
 ...tial-expression-rendered-unnamed-chunk-7-1.png} | Bin
 ...tial-expression-rendered-unnamed-chunk-7-2.png} | Bin
 ...expression-rendered-unnamed-chunk-8-1.png (new) | Bin 0 -> 20404 bytes
 ...xpression-rendered-unnamed-chunk-8-1.png (gone) | Bin 20304 -> 0 bytes
 ...8-extra-design-rendered-unnamed-chunk-10-1.png} | Bin
 ...8-extra-design-rendered-unnamed-chunk-11-1.png} | Bin
 ...8-extra-design-rendered-unnamed-chunk-11-2.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-5-1.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-5-2.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-6-1.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-7-1.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-8-1.png} | Bin
 ...08-extra-design-rendered-unnamed-chunk-9-1.png} | Bin
 index.md                                           |   4 +-
 md5sum.txt                                         |  23 +++--
 setup.md                                           |   2 +-
 34 files changed, 153 insertions(+), 135 deletions(-)
What does this mean? If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2023-05-17 15:14:59 +0000