GSVA for RNA-seq Part 1: Set up

[cansavvy]

Analysis Purpose

Adding an RNA-seq version of GSVA. This is part 1 of two. This involves the set up but stops before we deal with duplicate entrez IDs (duplicate dealing and GSVA run itself will be part 2).

369

Pull Request Stage

This is a Refined PR - needs polishing and details

The big picture was discussed on the draft PR #396

I've kept the tags to help guide review, after an initial review, I will delete them (unless you want me to delete them sooner).

**IDENTICAL TO MICROARRAY GSVA** means that until a different tag shows up, all the info there is 99% the same as whichever example is mentioned in the tag. Any differences I put in parenthesis like (except microarray. --> rnaseq)

Strategy

We did some rearrangements and simplifying on #396 Note that the intro to GSVA I have not touched at all. I'm ignoring that for now and we can mimic whatever is developed for #371

Concerns/Questions for reviewers:

• I think mostly the wording and comments are what need extra scrutiny.

Analysis Pull Request Check List (roughly in order):

Content checks

• [x] All {{BLANKS}} have been replaced with the correct content.
• [x] Sources are cited
• [ ] Seed is set (if applicable)

Formatting Checks

• [x] Removed any manual numbering of sections.
• [x] Removed any instances of chunk naming.
• [x] Comments and documentation are up to date.
• [x] All links have been checked and are properly formatted.

Add datasets to S3

• [x] Added data and metadata files to S3.

Docker/Snakemake rendering components

• [x] Added the .html link to the navigation bar.
• [x] Any not yet added packages needed for this analysis have been added to the Dockerfile and it successfully builds.