Ep2 setup

[ghar1821]

Hi guys,

I've written up episode 2. Link to the github issues: https://github.com/carpentries-incubator/bioc-rnaseq/issues/44.

I've tested the changes by running sandpaper::serve(), and everything seems to work fine.

Hopefully it is good! Let me know if what you think.

[github-actions[bot]]

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:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/carpentries-incubator/bioc-rnaseq/compare/md-outputs..md-outputs-PR-47

The following changes were observed in the rendered markdown documents:

 01-intro-to-rnaseq.md                      |   2 +-
 02-setup.md                                | 218 +++++++++++++++++++++++++++--
 fig/02_setup/data_folder.png (new)         | Bin 0 -> 67246 bytes
 fig/02_setup/folders_working_dir.png (new) | Bin 0 -> 61827 bytes
 fig/02_setup/rstudio_console.png (new)     | Bin 0 -> 154128 bytes
 fig/02_setup/rstudio_project.png (new)     | Bin 0 -> 95425 bytes
 md5sum.txt                                 |   4 +-
 7 files changed, 209 insertions(+), 15 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 2023-05-31 17:36:43 +0000

[jdrnevich]

@ghar1821 this looks great! Thanks so much for all your effort. I have one change that it might be easiest for you to do and then push/pull request again. In the Questions section at the top, you have "How to download a data set from Gene Expression Omnibus (GEO)?" But we are actually not covering that. Instead, I would change it to "How to download a data set from the internet and save as a file"

[ghar1821]

@ghar1821 this looks great! Thanks so much for all your effort. I have one change that it might be easiest for you to do and then push/pull request again. In the Questions section at the top, you have "How to download a data set from Gene Expression Omnibus (GEO)?" But we are actually not covering that. Instead, I would change it to "How to download a data set from the internet and save as a file"

Ah yes! Completely missed that. Thanks! I've made the changes in a new pull request: https://github.com/carpentries-incubator/bioc-rnaseq/pull/48