PR to address bioconductor lesson issues from first beta

[naupaka]

This is a PR to address issues raised in the first beta-pilot of the lesson (outlined in #142). All of the commits address problems identified in the bioconductor lesson.

It addresses:

• Fix broken screenshot of bioconductor homepage #163
• Header level is off on “Second, install the vcfR package from Bioconductor using BiocManager” #168
• Header level is off and broken screenshot on “Search for Bioconductor packages based on your analysis needs” #169
• We haven’t talked about packages anywhere else, and only mentioned base R briefly. We may need a bit more material to introduce why packages are necessary/useful etc. #170
• Installing packages from Bioconductor vs from CRAN) seems pretty nuanced and advanced - is there a way to simplify this for the learner? I think we hadn't introduced installing from CRAN yet, before talking about Bioconductor? #173
• Remove the final “challenge” box on this page. Looks like an unfinished note to developers of things that are already incorporated into this episode. #185
• Add a new challenge to this episode. Tracy had learners install a package of their choice from Bioconductor, but says “Feels risky to ask learners to install a package from the “wild” I’ve spent a fair amount of time running into trouble with dependencies, OS issues, etc.” Multiple learners had problems with installing packages, including some cases where our install of R wasn’t new enough. #186
• Learner says that Package that we installed didn’t show up in our package list. Why is this and should we add a warning / callout about it? #187
• Add a warning box about the long install process while vcfR is being installed due to many dependencies. #188

[naupaka]

@ytakemon @JasonJWilliamsNY @poterlowicz-lab This is now ready for review when you have a moment. Thanks!

[ytakemon]

I like this explanation! I noticed that we mention packages in the "R Basics continued" episode, but we don't explain it to this extent. I wonder if this would be a better fit in an earlier episode than in the Bioconductor one.

[naupaka]

Sure, I think that probably makes sense. This is related to #170 -- if @JasonJWilliamsNY is ok with it I can pull this description out from here, and do a PR of the content on the R Basic continued lesson.

[naupaka]

Never mind -- might as well move fast and break things, eh? I pulled out the paragraph in commit c28e053 and will PR it to the earlier lesson separately. @ytakemon let me know if there are any other adjustments you think I should make or if this is ready to merge.

[ytakemon]

Looks good to me! Merging.

[ytakemon]

The rest of the commits look great @naupaka! I'd be happy to merge this request once we had a chance to discuss my comment above.