add challenges to expl data analysis

[almutlue]

Changes:

• Extended challenge about consequences of more or less aggressive filtering
• New challenge about interpretations of PCA
• New challenge to color PCA by library sizes
• New challenge and short section (could definitely be extended in future) about iSEE and interactive exploratory data analysis

Fixes:

• Remove callout for contributions in exploratory data analysis part
• Do not evaluate last DE chunk to store DE results as csv. The csv. file was not used downstream and the output direction was missing.

[github-actions[bot]]

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: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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
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Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-81

The following changes were observed in the rendered markdown documents:

 04-exploratory-qc.md                               |  220 +-
 05-differential-expression.md                      |   55 -
 07-gene-set-analysis.md                            |    8 +-
 config.yaml (gone)                                 |   86 -
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 ...-analysis-rendered-unnamed-chunk-8-1.png (gone) |  Bin 28328 -> 0 bytes
 md5sum.txt                                         |   36 +-
 renv.lock (gone)                                   | 2776 --------------------
 48 files changed, 201 insertions(+), 2980 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 2023-09-13 16:14:44 +0000