Bioinformatics - KEGG Pathway Visualization in R

The final video in the pipeline!

Here we are going to look at the GO and KEGG pathways calculated from the DESeq2 object we previously created. We have to use `pathview`, `gage`, and several data sets from `gageData`. We also see the importance of exploring the results a little further when P53 pathway is upregulated as a whole but P53, while having higher levels in the P53+/+ samples, didn't show as much of an increase by treatment than did P53-/-.

Creating DESeq2 object:
   • Bioinformatics - Visualizing Counts Data  

Calculating Differentially Expressed genes:
   • Bioinformatics - Finding Differential...  

Series github with the subsampled data so the whole pipeline can be done on most computers.
https://github.com/ACSoupir/Bioinform...



I use these videos to practice speaking and teaching others about processes. If you have suggestions or recommendations for a better way to perform something, feel free to let me know! Science is collaborative and learning is the same.

The image at the bottom left of the thumbnail is modified from AllGenetics.EU.

Please consider contributing to my Patreon where I may do merch, gather ideas for future content, and have further discussions:
  / alexsoupir