Include LFC shrinkage and a volcano plot in bulk RNA-seq

[cbethell]

This issue is intended to track the progress of updating the bulk RNA-seq training material to include LFC shrinkage similarly to this section of a 2020-june-training supplemental notebook and to include a volcano plot similarly to this section of the same notebook.

This issue was opened per this point left on merged PR AlexsLemonade/2021-march-training#12,

An expanded version of differential expression analysis that includes LFC shrinkage and volcano plots (see: AlexsLemonade/training-admin#324). Part of the rationale for that is the set up that we do for the pathway analysis files right now and I also think it'd be neat to tie in a volcano plot because of what we cover in intro to R.

and these two points left on the potential bulk RNA-seq changes inspired by 2020 May and 2020 June trainings issue #240,

• Include LFC shrinkage (note to future self: this step is not instantaneous) and filtering by both FDR and LFC: https://alexslemonade.github.io/2020-june-training/supplemental_notebooks/2020-06-26_supplemental-notes.nb.html#shrunken_log2_foldchanges (related to this which got filed in the wrong place during the last workshop 🤷: AlexsLemonade/training-admin#324)
• Consider including a volcano plot which ties in nicely with the intro to R/tidyverse material: https://alexslemonade.github.io/2020-june-training/supplemental_notebooks/2020-06-26_supplemental-notes.nb.html#volcano_plot

[jaclyn-taroni]

Per data science team meeting notes comments, we want to do this for the 2021 March training. We can remove the heatmap that's currently in 05 and include LFC shrinkage and volcano plot in that notebook instead.