RNAseq analysis

[jaybee84]

This issue is for generating plots for RNASeq DEG analysis. This issue will be closed when all panels in the figures of the final paper can be regenerated using the markdown files or notebooks added to the pull request.

Please make sure the pull request satisfies the following checks:

• Input sample SynIDs are present in code
• All package dependencies are present in code
• All figure panels of the final figures are present, and can be regenerated by running the by an independent user
• Both raw markdown files and rendered final file are present in the pull request
• Authors are clearly stated in the raw code file
• Code is accompanied by comments or text to describe analytical steps