module 2 lab part 1- g:profiler - review and update

[risserlin]

No description provided.

[risserlin]

reviewed presentation associated with the lab.
Added example script/chapter for:

• running g:profiler from R - https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/run-gprofiler-from-r.html
• running GSEA from R - https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/run-gsea-from-within-r.html
• creating your own gmt file using ensembl - https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/create-gmt-file-from-ensembl.html

Added links in the presentation to examples -> need to add them to the physical lab as well.

[risserlin]

added automation bonus section as link https://risserlin.github.io/CBW_pathways_workshop_R_notebooks/run-gprofiler-from-r.html --> wondering if it would look better with all the text embedded in this book instead.

[risserlin]

TODO:
Update parameter screenshot to include WikiPathways --> gp3.png
Add step to set min gs size. It is not set to 3 in the tutorial.
Update filenames to reflect both min and max thresholds.
Update the results figures to reflect the latest db --> gp5.png, gp6.png, gp7.png, gp15.png
make sure the files created in the automation match the ones created in the lab.
Add info on get the version of the gmt file (and storing it in the filename) - same as mentioned in the automation version.