ORA RNA-seq: Part 1 - The Set Up

[cansavvy]

Analysis Purpose

Add an "RNA-seq" version of ORA pathway analysis. This PR adds the "Set Up" part 2 will add the actual ORA and plot making.

344

Pull Request Stage

This is a Refined PR - needs review of big concepts and outline. Draft Review occurred here: #381 not much changed.

To help reviewers save time, I'm still using slightly different tags to alert you to the few places that have changed in this module so far.

After your initial review, I will make a commit that deletes all these tags. (Unless you don't want the tags in the first place, then I can just delete them).

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

**REVIEW** doesn't mean it's 100% polished, but it does mean that it differs from the microarray example.

Strategy

Main changes from the Microarray are:

• We're using a WGCNA module gene list instead of DGE results.
• Conversion now is not gene symbols but entrez IDs
• Not danio rerio -> human

Most everything else is pretty identical to microarray ORA.

Concerns/Questions for reviewers:

I think wording and descriptions of the WGCNA analysis are the main focus here. Do they make sense but aren't going off the trail too much?

Analysis Pull Request Check List (roughly in order):

Content checks

• [x] All {{BLANKS}} have been replaced with the correct content.
• [x] Sources are cited
• [x] Seed is set (if applicable) -- not set here.

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.

[cansavvy]

Thanks for this review. I went ahead and ported over the relevant wording changes to microarray. There was really just one. But I also went ahead and addressed #393

Anything else left to address? @jashapiro